Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr3
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: 36364294
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2168405 characters in sequence are not A, C, G, or T
File 12 of 91
Found at i:3485139 original size:80 final size:79
Alignment explanation
Indices: 3485052--3485211 Score: 302
Period size: 80 Copynumber: 2.0 Consensus size: 79
3485042 CTAATATACA
3485052 ACATATATAAAAAAAAATGGGATAATTAACATATTAATTAATTAATTATATTTACATGTGAATTT
1 ACATATATAAAAAAAAATGGGATAATTAACATATTAATTAATTAATTATATTTACATGTGAATTT
3485117 AATAAAATAGTAAC
66 AATAAAATAGTAAC
3485131 ANCATATATAAAAAAAAATGGGATAATTAACATATTAATTAATTAATTATATTTACATGTGAATT
1 A-CATATATAAAAAAAAATGGGATAATTAACATATTAATTAATTAATTATATTTACATGTGAATT
*
3485196 TAATGAAATAGTAAC
65 TAATAAAATAGTAAC
3485211 A
1 A
3485212 TGCTAAAAGC
Statistics
Matches: 79, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
79 1 0.01
80 78 0.99
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.35
Consensus pattern (79 bp):
ACATATATAAAAAAAAATGGGATAATTAACATATTAATTAATTAATTATATTTACATGTGAATTT
AATAAAATAGTAAC
Found at i:3486092 original size:43 final size:43
Alignment explanation
Indices: 3486028--3486146 Score: 145
Period size: 43 Copynumber: 2.8 Consensus size: 43
3486018 ATAGAGATAG
* *
3486028 GATATTTTAAATTGAAACAAATTAAATTTAAA-A-AATAAATA
1 GATAATTTAAATTTAAACAAATTAAATTTAAATACAATAAATA
* **
3486069 -ATCCTTATTTAAATTTAAACAAATTAAATTTAAATACAATGGATA
1 GA---TAATTTAAATTTAAACAAATTAAATTTAAATACAATAAATA
3486114 GATAATTTAAATTTAAACAAATTAAATTTAAAT
1 GATAATTTAAATTTAAACAAATTAAATTTAAAT
3486147 TTATCCTATC
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
40 1 0.02
43 57 0.86
44 1 0.02
45 6 0.09
46 1 0.02
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.37
Consensus pattern (43 bp):
GATAATTTAAATTTAAACAAATTAAATTTAAATACAATAAATA
Found at i:3486095 original size:15 final size:15
Alignment explanation
Indices: 3486077--3486145 Score: 54
Period size: 15 Copynumber: 4.7 Consensus size: 15
3486067 TAATCCTTAT
3486077 TTAAATTTAAACAAA
1 TTAAATTTAAACAAA
*
3486092 TTAAATTTAAATACAA
1 TTAAATTTAAACA-AA
** * * *
3486108 -TGGA--TAGATAAT
1 TTAAATTTAAACAAA
3486120 TTAAATTTAAACAAA
1 TTAAATTTAAACAAA
3486135 TTAAATTTAAA
1 TTAAATTTAAA
3486146 TTTATCCTAT
Statistics
Matches: 40, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
12 1 0.03
13 7 0.17
15 30 0.75
16 2 0.05
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.36
Consensus pattern (15 bp):
TTAAATTTAAACAAA
Found at i:3486227 original size:15 final size:15
Alignment explanation
Indices: 3486207--3486236 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3486197 AATAATATCT
3486207 AATATTAATTAATTA
1 AATATTAATTAATTA
*
3486222 AATATTAGTTAATTA
1 AATATTAATTAATTA
3486237 TCCATAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
AATATTAATTAATTA
Found at i:3488190 original size:21 final size:21
Alignment explanation
Indices: 3488135--3488183 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
3488125 TACAAAAATA
3488135 TGTTACACGCCATGATTAGGT
1 TGTTACACGCCATGATTAGGT
*
3488156 TGTTACACGCCATGGTTAGGT
1 TGTTACACGCCATGATTAGGT
3488177 TGTTACA
1 TGTTACA
3488184 TACCATGTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.35
Consensus pattern (21 bp):
TGTTACACGCCATGATTAGGT
Found at i:3488238 original size:24 final size:24
Alignment explanation
Indices: 3488186--3488231 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
3488176 TTGTTACATA
*
3488186 CCATGTACAGAAACATGTGACACG
1 CCATGTACAAAAACATGTGACACG
3488210 CCATGTACAAAAACATGTGACA
1 CCATGTACAAAAACATGTGACA
3488232 TGTCATGGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.17
Consensus pattern (24 bp):
CCATGTACAAAAACATGTGACACG
Found at i:3488357 original size:29 final size:29
Alignment explanation
Indices: 3488318--3488394 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
3488308 GCCATGTTGA
3488318 AAAAAAATATTGTTGTTACACGCAATATT
1 AAAAAAATATTGTTGTTACACGCAATATT
* * * *
3488347 AAAAAAATATTATTATTACATGCCATATT
1 AAAAAAATATTGTTGTTACACGCAATATT
* *
3488376 -CAAAAACATTG-TGTTACAC
1 AAAAAAATATTGTTGTTACAC
3488395 TTTAATGTCT
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
27 6 0.15
28 8 0.21
29 25 0.64
ACGTcount: A:0.45, C:0.13, G:0.08, T:0.34
Consensus pattern (29 bp):
AAAAAAATATTGTTGTTACACGCAATATT
Found at i:3502961 original size:29 final size:28
Alignment explanation
Indices: 3502927--3503025 Score: 92
Period size: 28 Copynumber: 3.5 Consensus size: 28
3502917 GAAAAACCAA
* *
3502927 GTTACATGTCATGTTCCAAAAATAATGTT
1 GTTACACGCCATGTT-CAAAAATAATGTT
* * * *
3502956 GTTACATGCCATGCTCAAAAA-AATATC
1 GTTACACGCCATGTTCAAAAATAATGTT
* * * *
3502983 GTTACACGTCATTTTGAAAAATAAAGTT
1 GTTACACGCCATGTTCAAAAATAATGTT
3503011 GTTACACGCCATGTT
1 GTTACACGCCATGTT
3503026 TAAGGTGTTT
Statistics
Matches: 55, Mismatches: 14, Indels: 3
0.76 0.19 0.04
Matches are distributed among these distances:
27 20 0.36
28 22 0.40
29 13 0.24
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.33
Consensus pattern (28 bp):
GTTACACGCCATGTTCAAAAATAATGTT
Found at i:3502986 original size:27 final size:29
Alignment explanation
Indices: 3502927--3502988 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
3502917 GAAAAACCAA
* * * *
3502927 GTTACATGTCATGTTCCAAAAATAATGTT
1 GTTACATGCCATGCTCCAAAAATAATATC
3502956 GTTACATGCCATGCT-CAAAAA-AATATC
1 GTTACATGCCATGCTCCAAAAATAATATC
3502983 GTTACA
1 GTTACA
3502989 CGTCATTTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 10 0.34
28 6 0.21
29 13 0.45
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (29 bp):
GTTACATGCCATGCTCCAAAAATAATATC
Found at i:3503151 original size:97 final size:97
Alignment explanation
Indices: 3502983--3503200 Score: 283
Period size: 97 Copynumber: 2.2 Consensus size: 97
3502973 AAAAAATATC
* * * *
3502983 GTTACACGTCATTTTGAAAAATAAAGTTGTTACACGCCATGTTTAAGGTGTTTAACTCTAAAAGT
1 GTTACACGCCATATTG-AAAA-AAAGTTGTTACACGCCATGTTTAAAGTGTTTAACTCTAAAACT
* ** *
3503048 TTATATCTTGGTGAAATACAAAGATAGAAACCAA
64 TTATATCCTAATGAAACACAAAGATAGAAACCAA
* * * *
3503082 GTTACACGCCATGTTGAAAAAAAGTTGTTAGACGTCATGTTTAAAGTGTTTAACTCTAAGACTTT
1 GTTACACGCCATATTGAAAAAAAGTTGTTACACGCCATGTTTAAAGTGTTTAACTCTAAAACTTT
*
3503147 ATATCCTAATGAAACACAAAGATAGAGACCAA
66 ATATCCTAATGAAACACAAAGATAGAAACCAA
* *
3503179 GTTACACACCATATTTAAAAAA
1 GTTACACGCCATATTGAAAAAA
3503201 TTTTGTTGTC
Statistics
Matches: 104, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
97 86 0.83
98 4 0.04
99 14 0.13
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (97 bp):
GTTACACGCCATATTGAAAAAAAGTTGTTACACGCCATGTTTAAAGTGTTTAACTCTAAAACTTT
ATATCCTAATGAAACACAAAGATAGAAACCAA
Found at i:3503305 original size:33 final size:33
Alignment explanation
Indices: 3503260--3503324 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
3503250 CAGGTGCTTA
*
3503260 ACTCCAAAAGCTTATGTCTTAGTGAAATACAAT
1 ACTCCAAAAGCTTATGTCCTAGTGAAATACAAT
*
3503293 ACTCCAAGAGCTTATGTCCTAGTGAAATACAA
1 ACTCCAAAAGCTTATGTCCTAGTGAAATACAA
3503325 AGATAGAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (33 bp):
ACTCCAAAAGCTTATGTCCTAGTGAAATACAAT
Found at i:3524224 original size:11 final size:11
Alignment explanation
Indices: 3524203--3524272 Score: 52
Period size: 11 Copynumber: 6.1 Consensus size: 11
3524193 TTTTCAAAAT
3524203 AAAAAGAGAAA
1 AAAAAGAGAAA
* *
3524214 GAAAAGGGAAA
1 AAAAAGAGAAA
3524225 AAAAAGAAGAAA
1 AAAAAG-AGAAA
* *
3524237 GAGAAAAAAGGAA
1 -A-AAAAGAGAAA
*
3524250 AAGAAGA-AAA
1 AAAAAGAGAAA
3524260 AAAAAGAGGAAA
1 AAAAAGA-GAAA
3524272 A
1 A
3524273 CACAAGGAGC
Statistics
Matches: 44, Mismatches: 10, Indels: 9
0.70 0.16 0.14
Matches are distributed among these distances:
10 8 0.18
11 18 0.41
12 9 0.20
13 5 0.11
14 4 0.09
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
AAAAAGAGAAA
Found at i:3524232 original size:16 final size:16
Alignment explanation
Indices: 3524211--3524263 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
3524201 ATAAAAAGAG
*
3524211 AAAGAAAAGGGAAAAA
1 AAAGAAAAGAGAAAAA
3524227 AAAGAAGAA-AGAGAAAA
1 AAAGAA-AAGAGA-AAAA
*
3524244 AAGGAAAAGAAGAAAAA
1 AAAGAAAAG-AGAAAAA
3524261 AAA
1 AAA
3524264 AGAGGAAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
16 10 0.33
17 17 0.57
18 3 0.10
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (16 bp):
AAAGAAAAGAGAAAAA
Found at i:3524232 original size:20 final size:18
Alignment explanation
Indices: 3524216--3524271 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
3524206 AAGAGAAAGA
*
3524216 AAAGGGAAAAAAAAGAAG
1 AAAGAGAAAAAAAAGAAG
3524234 AAAGAGAAAAAAGGAA-AAG
1 AAAGAGAAAAAA--AAGAAG
*
3524253 -AAGA-AAAAAAAAGAGG
1 AAAGAGAAAAAAAAGAAG
3524269 AAA
1 AAA
3524272 ACACAAGGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
15 2 0.06
16 2 0.06
17 8 0.25
18 15 0.47
19 3 0.09
20 2 0.06
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (18 bp):
AAAGAGAAAAAAAAGAAG
Found at i:3524241 original size:9 final size:9
Alignment explanation
Indices: 3524203--3524262 Score: 52
Period size: 9 Copynumber: 6.6 Consensus size: 9
3524193 TTTTCAAAAT
3524203 AAAAAGAGAA
1 AAAAAGAG-A
*
3524213 AGAAAAGGGA
1 A-AAAAGAGA
*
3524223 AAAAAAAGA
1 AAAAAGAGA
*
3524232 AGAAAGAGA
1 AAAAAGAGA
3524241 AAAAAG-GA
1 AAAAAGAGA
3524249 AAAGAAGA-A
1 AAA-AAGAGA
3524258 AAAAA
1 AAAAA
3524263 AAGAGGAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
8 7 0.17
9 25 0.61
10 3 0.07
11 6 0.15
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (9 bp):
AAAAAGAGA
Found at i:3525636 original size:92 final size:93
Alignment explanation
Indices: 3525523--3525709 Score: 286
Period size: 93 Copynumber: 2.0 Consensus size: 93
3525513 GTGAGAAATT
* * *
3525523 AATTAAGTTCATAGAGACTTAATTAAATTAAAA-ACAACTGTTGTATTTAGAATTACAACTTAGT
1 AATTAAGTTCACAGAAACTTAATTAAATTAAAATACAACTGTTCTATTTAGAATTACAACTTAGT
* * * *
3525587 TTGGCTATATATATATGTTGTGTTAGCA
66 TTGGCTATATAAATATATTATATTAGCA
* *
3525615 AATTAAGTTCACAGAAACTTAATTAAATTAAAATATAACTGTTCTATTTAGAGTTACAACTTAGT
1 AATTAAGTTCACAGAAACTTAATTAAATTAAAATACAACTGTTCTATTTAGAATTACAACTTAGT
3525680 TTGGCTATATAAATATATTATATTAGCA
66 TTGGCTATATAAATATATTATATTAGCA
3525708 AA
1 AA
3525710 CTAAAAACTC
Statistics
Matches: 85, Mismatches: 9, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
92 31 0.36
93 54 0.64
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.39
Consensus pattern (93 bp):
AATTAAGTTCACAGAAACTTAATTAAATTAAAATACAACTGTTCTATTTAGAATTACAACTTAGT
TTGGCTATATAAATATATTATATTAGCA
Found at i:3528202 original size:14 final size:14
Alignment explanation
Indices: 3528179--3528242 Score: 69
Period size: 14 Copynumber: 4.6 Consensus size: 14
3528169 TTTTCAAAGT
3528179 AAAAAAAAAAGATG
1 AAAAAAAAAAGATG
* *
3528193 AAAAACAAAATA-G
1 AAAAAAAAAAGATG
* *
3528206 -AAAGAAAAAGAAG
1 AAAAAAAAAAGATG
3528219 AAAAAAAAAAGATG
1 AAAAAAAAAAGATG
3528233 AAAAACAAAA
1 AAAAA-AAAA
3528243 TAGAAAGAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
12 8 0.20
13 2 0.05
14 26 0.65
15 4 0.10
ACGTcount: A:0.80, C:0.03, G:0.12, T:0.05
Consensus pattern (14 bp):
AAAAAAAAAAGATG
Found at i:3528208 original size:13 final size:13
Alignment explanation
Indices: 3528192--3528248 Score: 55
Period size: 13 Copynumber: 4.3 Consensus size: 13
3528182 AAAAAAAGAT
3528192 GAAAAACAAAATA
1 GAAAAACAAAATA
3528205 GAAAGAA-AAAGA-A
1 GAAA-AACAAA-ATA
* *
3528218 GAAAAAAAAAAGA
1 GAAAAACAAAATA
3528231 TGAAAAACAAAATA
1 -GAAAAACAAAATA
3528245 GAAA
1 GAAA
3528249 GAAAAAGAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
12 3 0.08
13 20 0.54
14 14 0.38
ACGTcount: A:0.77, C:0.04, G:0.14, T:0.05
Consensus pattern (13 bp):
GAAAAACAAAATA
Found at i:3528209 original size:20 final size:20
Alignment explanation
Indices: 3528186--3528250 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
3528176 AGTAAAAAAA
3528186 AAAGATGAAAAACAAAATAG
1 AAAGATGAAAAACAAAATAG
* * * *
3528206 AAAGA-AAAAGAAGAAAAAAA
1 AAAGATGAAA-AACAAAATAG
3528226 AAAGATGAAAAACAAAATAG
1 AAAGATGAAAAACAAAATAG
3528246 AAAGA
1 AAAGA
3528251 AAAAGAAGAA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
19 3 0.09
20 29 0.83
21 3 0.09
ACGTcount: A:0.75, C:0.03, G:0.15, T:0.06
Consensus pattern (20 bp):
AAAGATGAAAAACAAAATAG
Found at i:3528234 original size:40 final size:40
Alignment explanation
Indices: 3528179--3528261 Score: 166
Period size: 40 Copynumber: 2.1 Consensus size: 40
3528169 TTTTCAAAGT
3528179 AAAAAAAAAAGATGAAAAACAAAATAGAAAGAAAAAGAAG
1 AAAAAAAAAAGATGAAAAACAAAATAGAAAGAAAAAGAAG
3528219 AAAAAAAAAAGATGAAAAACAAAATAGAAAGAAAAAGAAG
1 AAAAAAAAAAGATGAAAAACAAAATAGAAAGAAAAAGAAG
3528259 AAA
1 AAA
3528262 TAATAAATGC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.78, C:0.02, G:0.14, T:0.05
Consensus pattern (40 bp):
AAAAAAAAAAGATGAAAAACAAAATAGAAAGAAAAAGAAG
Found at i:3528260 original size:13 final size:13
Alignment explanation
Indices: 3528204--3528261 Score: 57
Period size: 13 Copynumber: 4.4 Consensus size: 13
3528194 AAAACAAAAT
3528204 AGAAAGAAAAAGA
1 AGAAAGAAAAAGA
*
3528217 AGAAAAAAAAAAGA
1 AG-AAAGAAAAAGA
*
3528231 TGAAA-AACAAA-A
1 AGAAAGAA-AAAGA
3528243 TAGAAAGAAAAAGA
1 -AGAAAGAAAAAGA
3528257 AGAAA
1 AGAAA
3528262 TAATAAATGC
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
12 3 0.08
13 20 0.54
14 14 0.38
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (13 bp):
AGAAAGAAAAAGA
Found at i:3540028 original size:11 final size:11
Alignment explanation
Indices: 3540012--3540062 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
3540002 CAATTTTATT
3540012 TTTTTTATTAA
1 TTTTTTATTAA
3540023 TTTTTTATTAA
1 TTTTTTATTAA
*
3540034 TTATTTAATTTAA
1 TT-TTTTA-TTAA
**
3540047 TTTAAT-TTAA
1 TTTTTTATTAA
3540057 TTTTTT
1 TTTTTT
3540063 TAGTTAAGTG
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
10 8 0.25
11 13 0.41
12 5 0.16
13 6 0.19
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTTTTATTAA
Found at i:3540069 original size:23 final size:22
Alignment explanation
Indices: 3540006--3540069 Score: 56
Period size: 23 Copynumber: 2.8 Consensus size: 22
3539996 CATCCCCAAT
* **
3540006 TTTATTTTTTTTATTAATTTTT
1 TTTAATTTTTTTATTAATTTAA
* *
3540028 TATTAATTATTTAATTTAATTTAA
1 T-TTAATTTTTTTA-TTAATTTAA
3540052 TTTAATTTTTTTAGTTAA
1 TTTAATTTTTTTA-TTAA
3540070 GTGTCTACAC
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
22 1 0.03
23 23 0.72
24 8 0.25
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTAATTTTTTTATTAATTTAA
Found at i:3547780 original size:3 final size:3
Alignment explanation
Indices: 3547772--3547801 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
3547762 TAGTTTACTC
*
3547772 TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3547802 GCTTTAGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:3551374 original size:15 final size:15
Alignment explanation
Indices: 3551338--3551374 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
3551328 ACTTACAATT
*
3551338 CTTTAAAAAAATCAA
1 CTTTAATAAAATCAA
3551353 CTTTAATAAAATCAA
1 CTTTAATAAAATCAA
3551368 CTTTAAT
1 CTTTAAT
3551375 GCCTTTCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (15 bp):
CTTTAATAAAATCAA
Found at i:3553836 original size:17 final size:18
Alignment explanation
Indices: 3553816--3553857 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
3553806 TTCTATAGAC
3553816 TTTTATTTTGTATT-TGA
1 TTTTATTTTGTATTGTGA
* * *
3553833 TTTTGTTTTTTATTGTTA
1 TTTTATTTTGTATTGTGA
3553851 TTTTATT
1 TTTTATT
3553858 AATTATTAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.14, C:0.00, G:0.10, T:0.76
Consensus pattern (18 bp):
TTTTATTTTGTATTGTGA
Found at i:3566429 original size:247 final size:247
Alignment explanation
Indices: 3566133--3566627 Score: 920
Period size: 247 Copynumber: 2.0 Consensus size: 247
3566123 TTGGCTTGAC
3566133 TTTTTTTTTTTTAGCTTAAAAGCTATTACAAAACTTTTATGAAAAATAATAGCTTGAAAGATAAT
1 TTTTTTTTTTTTAGCTTAAAAGCTATTACAAAACTTTTATGAAAAATAATAGCTTGAAAGATAAT
* *
3566198 ATATTTTAAAATAAAGTTAAAGTTGTTTGATAAATTTACTTTTTATAAACTCTTTTTTATATATA
66 ATATTTTAAAATAAAGTTAAAGTTGTTTGATAAATTTACTTTTTATAAACTCATTTTTATAGATA
*
3566263 AGTTGTTTGGCAAAATAACTTATATAAGCTCTAATTTTGGTTAAAATTACTATAAAGGGTATTTA
131 AGCTGTTTGGCAAAATAACTTATATAAGCTCTAATTTTGGTTAAAATTACTATAAAGGGTATTTA
3566328 ATAAATAACTTTCTATTAATCATAAATTCCTTTGTTCAAAATGGAAAAAAGT
196 ATAAATAACTTTCTATTAATCATAAATTCCTTTGTTCAAAATGGAAAAAAGT
3566380 TNTTTTTTTTTTTAGC-TAAAAGCTATTACAAAACTTTTATGAAAAATAATAGCTTGAAAGATAA
1 T-TTTTTTTTTTTAGCTTAAAAGCTATTACAAAACTTTTATGAAAAATAATAGCTTGAAAGATAA
3566444 TATATTTTAAAATAAAGTTAAAGTTGTTTGATAAATTTACTTTTTATAAACTCATTTTTATAGAT
65 TATATTTTAAAATAAAGTTAAAGTTGTTTGATAAATTTACTTTTTATAAACTCATTTTTATAGAT
* * *
3566509 AAGCTGTTTGGCAAAATAACTTATATAAGCTCTAATTTTGGTTAAAATTATTATATAGGGTGTTT
130 AAGCTGTTTGGCAAAATAACTTATATAAGCTCTAATTTTGGTTAAAATTACTATAAAGGGTATTT
3566574 AATAAATAACTTTCTATTAATCATAAATTCCTTTGTTCAAAATGGAAAAAAGT
195 AATAAATAACTTTCTATTAATCATAAATTCCTTTGTTCAAAATGGAAAAAAGT
3566627 T
1 T
3566628 AACTTTATTT
Statistics
Matches: 241, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
247 227 0.94
248 14 0.06
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43
Consensus pattern (247 bp):
TTTTTTTTTTTTAGCTTAAAAGCTATTACAAAACTTTTATGAAAAATAATAGCTTGAAAGATAAT
ATATTTTAAAATAAAGTTAAAGTTGTTTGATAAATTTACTTTTTATAAACTCATTTTTATAGATA
AGCTGTTTGGCAAAATAACTTATATAAGCTCTAATTTTGGTTAAAATTACTATAAAGGGTATTTA
ATAAATAACTTTCTATTAATCATAAATTCCTTTGTTCAAAATGGAAAAAAGT
Found at i:3570487 original size:22 final size:22
Alignment explanation
Indices: 3570447--3570489 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3570437 TTATTTCTTT
*
3570447 TTTTTTTCTGTTTTGTTTTTAA
1 TTTTTTTCTATTTTGTTTTTAA
*
3570469 TTTTTTTCTATTGTTTTTTTT
1 TTTTTTTCTATT-TTGTTTTT
3570490 TAGGTTTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.07, C:0.05, G:0.07, T:0.81
Consensus pattern (22 bp):
TTTTTTTCTATTTTGTTTTTAA
Found at i:3570643 original size:13 final size:13
Alignment explanation
Indices: 3570622--3570653 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
3570612 AAAAAAATAT
*
3570622 TAATATAAACATA
1 TAATGTAAACATA
3570635 TAATGTAAACATA
1 TAATGTAAACATA
3570648 TAATGT
1 TAATGT
3570654 TCAAGACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.34
Consensus pattern (13 bp):
TAATGTAAACATA
Found at i:3577726 original size:34 final size:35
Alignment explanation
Indices: 3577686--3577768 Score: 89
Period size: 34 Copynumber: 2.4 Consensus size: 35
3577676 AACTTTCCCT
* *
3577686 CTCTAACCGGTGGCAA-CAAAACCCAAACTTTGTC
1 CTCTAACCGGCGGCAACCAAAACCAAAACTTTGTC
* * *
3577720 CTCTAACTGGCAG-AACCAAAACCAAAACTTTTTC
1 CTCTAACCGGCGGCAACCAAAACCAAAACTTTGTC
* *
3577754 TTCTAACCGGGGGCA
1 CTCTAACCGGCGGCA
3577769 CTAAACCTAG
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
33 2 0.05
34 35 0.92
35 1 0.03
ACGTcount: A:0.33, C:0.30, G:0.16, T:0.22
Consensus pattern (35 bp):
CTCTAACCGGCGGCAACCAAAACCAAAACTTTGTC
Found at i:3578548 original size:50 final size:50
Alignment explanation
Indices: 3578471--3578925 Score: 583
Period size: 50 Copynumber: 9.1 Consensus size: 50
3578461 AAGCTCGACA
* * * * * **
3578471 ACTTTGAAATTCATTTTGAAACATAAACAACTCCTCATCTGAGGTTTTTTC
1 ACTTT-AAAATCAATTTGAAAAATAAACAACTCCTCATCCGAGGCTTTACC
*
3578522 ACTTTAAAATCAATTTGAAAAATAAACAACTCCTCATCCGAGGCTATACC
1 ACTTTAAAATCAATTTGAAAAATAAACAACTCCTCATCCGAGGCTTTACC
* * **
3578572 ACTTTTAAAATCAACTTTGAACAATAAACAACTCCTCATCCGAGGCTCTATT
1 AC-TTTAAAATCAA-TTTGAAAAATAAACAACTCCTCATCCGAGGCTTTACC
** * * *
3578624 GTTTTAAAATCATTTTGAAAAATAAATAACTCCTCATCCGAGGCTCTACC
1 ACTTTAAAATCAATTTGAAAAATAAACAACTCCTCATCCGAGGCTTTACC
* * * *
3578674 ACTTTAAAATCAATTT-AATAAATAAATAACTCCTCATCCGAAGCTCTACT
1 ACTTTAAAATCAATTTGAA-AAATAAACAACTCCTCATCCGAGGCTTTACC
* * *
3578724 ACTTTAAAATCAATTTGAAAAATAAATAACTCCTCATCTGAGGCTCTACC
1 ACTTTAAAATCAATTTGAAAAATAAACAACTCCTCATCCGAGGCTTTACC
*
3578774 ACTTTAAAATCAATTAGAAAAATAAACAACTCCTCAT-CGAGGCTTTACC
1 ACTTTAAAATCAATTTGAAAAATAAACAACTCCTCATCCGAGGCTTTACC
* *
3578823 ACTTTAAAATCAATTTG-AACATAAACAACTCCTCATCCGAGGCTTTCCC
1 ACTTTAAAATCAATTTGAAAAATAAACAACTCCTCATCCGAGGCTTTACC
* * *
3578872 ACTTTAAAATCAATTTGAAAAATAAACAACTCCTCATCTGAGGCTCTACA
1 ACTTTAAAATCAATTTGAAAAATAAACAACTCCTCATCCGAGGCTTTACC
3578922 ACTT
1 ACTT
3578926 CTGATTTTCC
Statistics
Matches: 359, Mismatches: 39, Indels: 13
0.87 0.09 0.03
Matches are distributed among these distances:
48 18 0.05
49 56 0.16
50 224 0.62
51 28 0.08
52 33 0.09
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (50 bp):
ACTTTAAAATCAATTTGAAAAATAAACAACTCCTCATCCGAGGCTTTACC
Found at i:3579786 original size:9 final size:9
Alignment explanation
Indices: 3579772--3579817 Score: 67
Period size: 9 Copynumber: 5.1 Consensus size: 9
3579762 TCAACTTGAA
3579772 TTTCTTTTT
1 TTTCTTTTT
3579781 TTTCTTTTT
1 TTTCTTTTT
3579790 TTTCTCTTTT
1 TTTCT-TTTT
*
3579800 TTT-TTCTT
1 TTTCTTTTT
3579808 TTTCTTTTT
1 TTTCTTTTT
3579817 T
1 T
3579818 GTTTTTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
8 6 0.18
9 20 0.61
10 7 0.21
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:3592806 original size:28 final size:29
Alignment explanation
Indices: 3592748--3592813 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
3592738 GTAAATTTTT
** *
3592748 AAAAATTACACTTTTACCCCTGTAAAGTG
1 AAAAATTACACTTTTACCCCTAAAAACTG
**
3592777 AAAAATTACGTTTTTACCCC-AAAAACTG
1 AAAAATTACACTTTTACCCCTAAAAACTG
3592805 AAAAATTAC
1 AAAAATTAC
3592814 CCATAGACAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 14 0.44
29 18 0.56
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.29
Consensus pattern (29 bp):
AAAAATTACACTTTTACCCCTAAAAACTG
Found at i:3595690 original size:35 final size:35
Alignment explanation
Indices: 3595608--3595690 Score: 87
Period size: 35 Copynumber: 2.4 Consensus size: 35
3595598 TCCTTTACCA
* * *
3595608 CCGATCAGATCTTCCCTCTCTCTATCTCTTCGGCG
1 CCGACCAGGTCTTCCCTCTCTCTATCTCTTCAGCG
** * *
3595643 TTGACC-GAGTCTTCCCTCTCTCTATCTGTTCAGTG
1 CCGACCAG-GTCTTCCCTCTCTCTATCTCTTCAGCG
3595678 CCGACCAGGTCTT
1 CCGACCAGGTCTT
3595691 GTCCTCTCCC
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
34 1 0.03
35 35 0.95
36 1 0.03
ACGTcount: A:0.12, C:0.36, G:0.17, T:0.35
Consensus pattern (35 bp):
CCGACCAGGTCTTCCCTCTCTCTATCTCTTCAGCG
Found at i:3595864 original size:34 final size:34
Alignment explanation
Indices: 3595824--3595912 Score: 135
Period size: 34 Copynumber: 2.6 Consensus size: 34
3595814 TTTCCCTCTT
3595824 TAACTGGCGGCAACAAAACCCAAACTTTGTCCAC
1 TAACTGGCGGCAACAAAACCCAAACTTTGTCCAC
* *
3595858 TAACTGGCGGTAACAAAACCCAAACTTTGTCCTC
1 TAACTGGCGGCAACAAAACCCAAACTTTGTCCAC
* *
3595892 TAACCGGCGGC-ACTAAACCCA
1 TAACTGGCGGCAACAAAACCCA
3595913 GGCTTTAACA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 9 0.18
34 41 0.82
ACGTcount: A:0.34, C:0.33, G:0.16, T:0.18
Consensus pattern (34 bp):
TAACTGGCGGCAACAAAACCCAAACTTTGTCCAC
Found at i:3596364 original size:11 final size:10
Alignment explanation
Indices: 3596341--3596402 Score: 61
Period size: 11 Copynumber: 5.7 Consensus size: 10
3596331 CGTACAGCTC
*
3596341 TTTTTTTTAT
1 TTTTTTTTCT
*
3596351 TTTTTCTTCT
1 TTTTTTTTCT
3596361 TTTTTTGTTCAT
1 TTTTTT-TTC-T
3596373 TTTTTGTTTCT
1 TTTTT-TTTCT
3596384 TGTTTTTTTCT
1 T-TTTTTTTCT
3596395 CTTTTTTT
1 -TTTTTTT
3596403 ACTATTATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
10 13 0.30
11 16 0.36
12 14 0.32
13 1 0.02
ACGTcount: A:0.03, C:0.10, G:0.05, T:0.82
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:3596399 original size:23 final size:21
Alignment explanation
Indices: 3596341--3596401 Score: 54
Period size: 23 Copynumber: 2.8 Consensus size: 21
3596331 CGTACAGCTC
*
3596341 TTTTTTTT-ATTTTTTCTTCT
1 TTTTTTTTCTTTTTTTCTTCT
3596361 TTTTTTGTTCATTTTTTGT-TTCT
1 TTTTTT-TTC-TTTTTT-TCTTCT
3596384 TGTTTTTTTCTCTTTTTT
1 T-TTTTTTTCT-TTTTTT
3596402 TACTATTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
20 6 0.18
21 2 0.06
22 2 0.06
23 18 0.53
24 6 0.18
ACGTcount: A:0.03, C:0.10, G:0.05, T:0.82
Consensus pattern (21 bp):
TTTTTTTTCTTTTTTTCTTCT
Found at i:3600073 original size:20 final size:20
Alignment explanation
Indices: 3600048--3600086 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3600038 TATTATGGAA
3600048 AATATATAAAAT-AATAATAT
1 AATATA-AAAATAAATAATAT
*
3600068 AATATAACAATAAATAATA
1 AATATAAAAATAAATAATA
3600087 AAAGTAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (20 bp):
AATATAAAAATAAATAATAT
Found at i:3601397 original size:31 final size:28
Alignment explanation
Indices: 3601335--3601399 Score: 76
Period size: 31 Copynumber: 2.2 Consensus size: 28
3601325 ACTTTTTCAC
*
3601335 TTAAGGGTAAACATTTCAATTGTAACAA
1 TTAAGGGTAAACATTTCAATTCTAACAA
* *
3601363 TTAAGGGTCAAACATTTTTAATTTCTTACAA
1 TTAAGGGT-AAACA-TTTCAA-TTCTAACAA
3601394 TTAAGG
1 TTAAGG
3601400 ACTAAGTTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 8 0.26
29 5 0.16
30 5 0.16
31 13 0.42
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (28 bp):
TTAAGGGTAAACATTTCAATTCTAACAA
Found at i:3613510 original size:50 final size:52
Alignment explanation
Indices: 3613455--3613645 Score: 203
Period size: 51 Copynumber: 3.7 Consensus size: 52
3613445 GCCCGTTTTG
* * * *
3613455 GAGTG-AAAGAGGGAAATCCGGT-TTTGAGTGGCCGACGTTAGAGAGAAAGT
1 GAGTGAAAAAAGGGAGATCCGGTCTTTGGGTGGCCGACGTTAGAGAGAGAGT
* * * *
3613505 GAGTGAAAAAAAGGAGATCCGTTCTTTGGGGTGGCCGCCGGTA-AGAGAGAGT
1 GAGTGAAAAAAGGGAGATCCGGTCTTT-GGGTGGCCGACGTTAGAGAGAGAGT
* ** * *
3613557 GAGTG-AAAGAGGGAGATTTGAT-TTTGGGTGGCTGACGTTAGAGAGAGAGT
1 GAGTGAAAAAAGGGAGATCCGGTCTTTGGGTGGCCGACGTTAGAGAGAGAGT
*
3613607 GAGTGAAAAAAGGGAGATCCGGTCTTTGGGAGAGCCGAC
1 GAGTGAAAAAAGGGAGATCCGGTCTTTGGGTG-GCCGAC
3613646 CGACAGTAGA
Statistics
Matches: 112, Mismatches: 22, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
49 12 0.11
50 22 0.20
51 38 0.34
52 23 0.21
53 17 0.15
ACGTcount: A:0.30, C:0.10, G:0.39, T:0.20
Consensus pattern (52 bp):
GAGTGAAAAAAGGGAGATCCGGTCTTTGGGTGGCCGACGTTAGAGAGAGAGT
Found at i:3614561 original size:3 final size:3
Alignment explanation
Indices: 3614555--3614602 Score: 51
Period size: 3 Copynumber: 15.0 Consensus size: 3
3614545 TTTAAAAAAA
* *
3614555 AAT AAT AAAT AAAT AAT AAT AAAT AAA AAT AAT AAT AAT AAT GAT AAT
1 AAT AAT -AAT -AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
3614603 TCAAATATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
3 29 0.74
4 10 0.26
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:3614568 original size:27 final size:27
Alignment explanation
Indices: 3614547--3614601 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
3614537 AAAATCATTT
3614547 TAAAAAAAAATAATAAATAAATAATAA
1 TAAAAAAAAATAATAAATAAATAATAA
* *
3614574 TAAATAAAAATAAT-AAT-AATAATGA
1 TAAAAAAAAATAATAAATAAATAATAA
3614599 TAA
1 TAA
3614602 TTCAAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 10 0.38
26 3 0.12
27 13 0.50
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (27 bp):
TAAAAAAAAATAATAAATAAATAATAA
Found at i:3614590 original size:19 final size:21
Alignment explanation
Indices: 3614559--3614621 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 21
3614549 AAAAAAAATA
3614559 ATAAATAAATAATAATAAATA
1 ATAAATAAATAATAATAAATA
3614580 A-AAAT-AATAATAATAATGATA
1 ATAAATAAATAATAATAA--ATA
*
3614601 ATTCAAATATAT-ATAATAAAT
1 A-T-AAATAAATAATAATAAAT
3614622 TTGTGAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
19 11 0.31
20 4 0.11
21 5 0.14
22 2 0.06
24 11 0.31
25 2 0.06
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (21 bp):
ATAAATAAATAATAATAAATA
Found at i:3616611 original size:17 final size:17
Alignment explanation
Indices: 3616579--3616612 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3616569 CAAAAAAAGG
**
3616579 AAAAAGAAAATTAAAAA
1 AAAAAGAAAAGGAAAAA
3616596 AAAAAGAAAAGGAAAAA
1 AAAAAGAAAAGGAAAAA
3616613 CAAAGATCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (17 bp):
AAAAAGAAAAGGAAAAA
Found at i:3623260 original size:143 final size:142
Alignment explanation
Indices: 3623003--3623621 Score: 1033
Period size: 143 Copynumber: 4.3 Consensus size: 142
3622993 AACCACTTTC
* * *
3623003 AAACCTCCGGGTAATTAATGTCAAGATTTTTTAAAGTTACGTTGTCTCAGTTTTCTAGAAGCCAC
1 AAACCTCCGGGTAATTAATGTCAAGATTTTTTAAAGTTACGTTGCCTCAGTTTTCGAGGAGCCAC
* *
3623068 ATTTCCTAAATCCTCCGGGTACCTTCTGAAGACCTCCGGGCACATTATTCTCTTAAATCTTCCGG
66 ATTTCCTAAATCCTCCGGGTACATTCTGAAGACCTCCGGGCACATTATTCTCTTAAATCCTCCGG
*
3623133 GTGTATCTTCTA
131 GTGCATCTTCTA
*
3623145 AAACCTCCGGGTAATTAATGTCAAGATTTTTTAAAAGTTAGGTTGCCTCAGTTTTCGAGGAGCCA
1 AAACCTCCGGGTAATTAATGTCAAGATTTTTT-AAAGTTACGTTGCCTCAGTTTTCGAGGAGCCA
* * *
3623210 CATTTCCTAAATCCTCCGGATACCTTCTGAAGACCTCCGGGCATATTATTCTCTTAAATCCTCCG
65 CATTTCCTAAATCCTCCGGGTACATTCTGAAGACCTCCGGGCACATTATTCTCTTAAATCCTCCG
3623275 GGTGCATCTTCTA
130 GGTGCATCTTCTA
* *
3623288 AAACCTCTGGGTAATTAATGTCAAGATTTTTT-AAGTTACGTTGTCTCAGTTTTCGAGGAGCCAC
1 AAACCTCCGGGTAATTAATGTCAAGATTTTTTAAAGTTACGTTGCCTCAGTTTTCGAGGAGCCAC
*
3623352 ATTTCCTAAATCCTCCGGGTACATTCTGAAGACCTCCGGGCACATTATTCTCTTAAATCCTCTAG
66 ATTTCCTAAATCCTCCGGGTACATTCTGAAGACCTCCGGGCACATTATTCTCTTAAATCCTC-CG
3623417 GGTGCATCTTCTA
130 GGTGCATCTTCTA
* * *
3623430 AAAACTCCGGATAATTAATGTCAAGATTTTTTAAAAGTTAGGTTGCCTCAGTTTTCGAGGAGCCA
1 AAACCTCCGGGTAATTAATGTCAAGATTTTTT-AAAGTTACGTTGCCTCAGTTTTCGAGGAGCCA
* *
3623495 CATTTCCTAAATCCTCCGGGTACATTCTAAAGACCTCCGAGCACATTATTCTCTTAAATCCTCCG
65 CATTTCCTAAATCCTCCGGGTACATTCTGAAGACCTCCGGGCACATTATTCTCTTAAATCCTCCG
3623560 GGTGCATCTTCTA
130 GGTGCATCTTCTA
*
3623573 AAACCTCCGGGTAATTAGTGTCAAGATTTTTTAAAGTTACGTTGCCTCA
1 AAACCTCCGGGTAATTAATGTCAAGATTTTTTAAAGTTACGTTGCCTCA
3623622 ACTTTGAGGA
Statistics
Matches: 446, Mismatches: 27, Indels: 8
0.93 0.06 0.02
Matches are distributed among these distances:
141 89 0.20
142 91 0.20
143 176 0.39
144 90 0.20
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (142 bp):
AAACCTCCGGGTAATTAATGTCAAGATTTTTTAAAGTTACGTTGCCTCAGTTTTCGAGGAGCCAC
ATTTCCTAAATCCTCCGGGTACATTCTGAAGACCTCCGGGCACATTATTCTCTTAAATCCTCCGG
GTGCATCTTCTA
Found at i:3623633 original size:285 final size:285
Alignment explanation
Indices: 3623003--3623621 Score: 1078
Period size: 285 Copynumber: 2.2 Consensus size: 285
3622993 AACCACTTTC
* *
3623003 AAACCTCCGGGTAATTAATGTCAAGATTTTTTAAAGTTACGTTGTCTCAGTTTTCTAGAAGCCAC
1 AAACCTCCGGGTAATTAATGTCAAGATTTTTTAAAGTTACGTTGTCTCAGTTTTCGAGGAGCCAC
* * *
3623068 ATTTCCTAAATCCTCCGGGTACCTTCTGAAGACCTCCGGGCACATTATTCTCTTAAATCTTCCGG
66 ATTTCCTAAATCCTCCGGGTACATTCTGAAGACCTCCGGGCACATTATTCTCTTAAATCCTCAGG
* * *
3623133 GTGTATCTTCTAAAACCTCCGGGTAATTAATGTCAAGATTTTTTAAAAGTTAGGTTGCCTCAGTT
131 GTGCATCTTCTAAAAACTCCGGATAATTAATGTCAAGATTTTTTAAAAGTTAGGTTGCCTCAGTT
* * * *
3623198 TTCGAGGAGCCACATTTCCTAAATCCTCCGGATACCTTCTGAAGACCTCCGGGCATATTATTCTC
196 TTCGAGGAGCCACATTTCCTAAATCCTCCGGATACATTCTAAAGACCTCCGAGCACATTATTCTC
3623263 TTAAATCCTCCGGGTGCATCTTCTA
261 TTAAATCCTCCGGGTGCATCTTCTA
*
3623288 AAACCTCTGGGTAATTAATGTCAAGATTTTTT-AAGTTACGTTGTCTCAGTTTTCGAGGAGCCAC
1 AAACCTCCGGGTAATTAATGTCAAGATTTTTTAAAGTTACGTTGTCTCAGTTTTCGAGGAGCCAC
3623352 ATTTCCTAAATCCTCCGGGTACATTCTGAAGACCTCCGGGCACATTATTCTCTTAAATCCTCTAG
66 ATTTCCTAAATCCTCCGGGTACATTCTGAAGACCTCCGGGCACATTATTCTCTTAAATCCTC-AG
3623417 GGTGCATCTTCTAAAAACTCCGGATAATTAATGTCAAGATTTTTTAAAAGTTAGGTTGCCTCAGT
130 GGTGCATCTTCTAAAAACTCCGGATAATTAATGTCAAGATTTTTTAAAAGTTAGGTTGCCTCAGT
*
3623482 TTTCGAGGAGCCACATTTCCTAAATCCTCCGGGTACATTCTAAAGACCTCCGAGCACATTATTCT
195 TTTCGAGGAGCCACATTTCCTAAATCCTCCGGATACATTCTAAAGACCTCCGAGCACATTATTCT
3623547 CTTAAATCCTCCGGGTGCATCTTCTA
260 CTTAAATCCTCCGGGTGCATCTTCTA
* *
3623573 AAACCTCCGGGTAATTAGTGTCAAGATTTTTTAAAGTTACGTTGCCTCA
1 AAACCTCCGGGTAATTAATGTCAAGATTTTTTAAAGTTACGTTGTCTCA
3623622 ACTTTGAGGA
Statistics
Matches: 315, Mismatches: 17, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
284 90 0.29
285 210 0.67
286 15 0.05
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (285 bp):
AAACCTCCGGGTAATTAATGTCAAGATTTTTTAAAGTTACGTTGTCTCAGTTTTCGAGGAGCCAC
ATTTCCTAAATCCTCCGGGTACATTCTGAAGACCTCCGGGCACATTATTCTCTTAAATCCTCAGG
GTGCATCTTCTAAAAACTCCGGATAATTAATGTCAAGATTTTTTAAAAGTTAGGTTGCCTCAGTT
TTCGAGGAGCCACATTTCCTAAATCCTCCGGATACATTCTAAAGACCTCCGAGCACATTATTCTC
TTAAATCCTCCGGGTGCATCTTCTA
Found at i:3623693 original size:85 final size:84
Alignment explanation
Indices: 3623550--3623718 Score: 311
Period size: 85 Copynumber: 2.0 Consensus size: 84
3623540 TTATTCTCTT
3623550 AAATCCTCCGGGTGCATCTTCTAAAACCTCCGGGTAATTAGTGTCAAGATTTTTTAAAGTTACGT
1 AAATCCTCCGGGTGCATCTTCTAAAACCTCCGGGTAATTAGTGTCAAGATTTTTTAAAGTTACGT
3623615 TGCCTCAACTTTGAGGAGC
66 TGCCTCAACTTTGAGGAGC
* *
3623634 NAAATCCTCCGGGTGCATTTTCTAAAACCTCCGGGTAATTAGTGTCAAGATTTTTTAAAGTTATG
1 -AAATCCTCCGGGTGCATCTTCTAAAACCTCCGGGTAATTAGTGTCAAGATTTTTTAAAGTTACG
3623699 TTGCCTCAACTTTGAGGAGC
65 TTGCCTCAACTTTGAGGAGC
3623719 CTCATTTAAA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 82 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.33
Consensus pattern (84 bp):
AAATCCTCCGGGTGCATCTTCTAAAACCTCCGGGTAATTAGTGTCAAGATTTTTTAAAGTTACGT
TGCCTCAACTTTGAGGAGC
Found at i:3623747 original size:5 final size:5
Alignment explanation
Indices: 3623726--3623835 Score: 86
Period size: 5 Copynumber: 21.6 Consensus size: 5
3623716 AGCCTCATTT
*
3623726 AAACA AAA-A AAATA AAAC- AAA-A AAACAA AAACA AAACA AAACAA AAACA
1 AAACA AAACA AAACA AAACA AAACA AAAC-A AAACA AAACA AAAC-A AAACA
* * *
3623775 AAACA CAAA-A AAAAA CAAACA AACACA AAA-A AAAAA AAAGAA AAACA
1 AAACA -AAACA AAACA -AAACA AA-ACA AAACA AAACA AAA-CA AAACA
3623822 GAAACA AAACA AAA
1 -AAACA AAACA AAA
3623836 ACACAAAAAA
Statistics
Matches: 90, Mismatches: 3, Indels: 24
0.77 0.03 0.21
Matches are distributed among these distances:
4 17 0.19
5 41 0.46
6 32 0.36
ACGTcount: A:0.83, C:0.15, G:0.02, T:0.01
Consensus pattern (5 bp):
AAACA
Found at i:3623748 original size:6 final size:6
Alignment explanation
Indices: 3623746--3623848 Score: 87
Period size: 5 Copynumber: 17.8 Consensus size: 6
3623736 AATAAAACAA
3623746 AAAAAC AAAAAC -AAAAC -AAAAC AAAAAC -AAAAC ACAAAA- AAAAAC
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC A-AAAAC AAAAAC
* * *
3623791 AAACAAAC ACAAA- AAAAA- AAAAAG AAAAAC AGAAAC -AAAAC AAAAAC
1 -AA-AAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC
3623838 ACAAAA- AAAAA
1 A-AAAAC AAAAA
3623849 GAAAGAGCTT
Statistics
Matches: 83, Mismatches: 5, Indels: 19
0.78 0.05 0.18
Matches are distributed among these distances:
5 36 0.43
6 32 0.39
7 11 0.13
8 4 0.05
ACGTcount: A:0.83, C:0.16, G:0.02, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:3623813 original size:41 final size:39
Alignment explanation
Indices: 3623730--3623848 Score: 97
Period size: 37 Copynumber: 3.2 Consensus size: 39
3623720 TCATTTAAAC
* *
3623730 AAAAAAAATAAA-ACAAAAAAACAAAAAC--AAAACAAA
1 AAAAAAAAAAAACACAAAAAAAAAAAAACAAAAAACAAA
* * * *
3623766 ACAAAAACAAAACACAAAAAAAAACAAAC-AAACACAAA
1 AAAAAAAAAAAACACAAAAAAAAAAAAACAAAAAACAAA
* * *
3623804 AAAAAAAAAAGAA-A-AACAGAAACAAAACAAAAACACAAA
1 AAAAAAAAAA-AACACAAAAAAAAAAAAACAAAAA-ACAAA
3623843 AAAAAA
1 AAAAAA
3623849 GAAAGAGCTT
Statistics
Matches: 65, Mismatches: 13, Indels: 7
0.76 0.15 0.08
Matches are distributed among these distances:
36 9 0.14
37 24 0.37
38 19 0.29
39 13 0.20
ACGTcount: A:0.83, C:0.14, G:0.02, T:0.01
Consensus pattern (39 bp):
AAAAAAAAAAAACACAAAAAAAAAAAAACAAAAAACAAA
Found at i:3623819 original size:47 final size:47
Alignment explanation
Indices: 3623732--3623846 Score: 146
Period size: 48 Copynumber: 2.4 Consensus size: 47
3623722 ATTTAAACAA
3623732 AAAAAATAAAACAAAAAAACAAAAACAAAACAAAACAAAAACA-AAAC
1 AAAAAA-AAAACAAAAAAACAAAAACAAAACAAAACAAAAACAGAAAC
*
3623779 ACAAAAAAAAACAAACAAACACAAAAA-AAAA-AAAAGAAAAACAGAAAC
1 A-AAAAAAAAACAAA-AAA-ACAAAAACAAAACAAAACAAAAACAGAAAC
3623827 AAAACAAAAACACAAAAAAA
1 AAAA-AAAAA-ACAAAAAAA
3623847 AAGAAAGAGC
Statistics
Matches: 61, Mismatches: 1, Indels: 12
0.82 0.01 0.16
Matches are distributed among these distances:
47 24 0.39
48 25 0.41
49 12 0.20
ACGTcount: A:0.83, C:0.15, G:0.02, T:0.01
Consensus pattern (47 bp):
AAAAAAAAAACAAAAAAACAAAAACAAAACAAAACAAAAACAGAAAC
Found at i:3623867 original size:1 final size:1
Alignment explanation
Indices: 3623730--3623848 Score: 58
Period size: 1 Copynumber: 119.0 Consensus size: 1
3623720 TCATTTAAAC
* * * * * * * * * * *
3623730 AAAAAAAATAAAACAAAAAAACAAAAACAAAACAAAACAAAAACAAAACACAAAAAAAAACAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * * * *
3623795 AAACACAAAAAAAAAAAAAGAAAAACAGAAACAAAACAAAAACACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3623849 GAAAGAGCTT
Statistics
Matches: 78, Mismatches: 40, Indels: 0
0.66 0.34 0.00
Matches are distributed among these distances:
1 78 1.00
ACGTcount: A:0.83, C:0.14, G:0.02, T:0.01
Consensus pattern (1 bp):
A
Found at i:3624310 original size:14 final size:14
Alignment explanation
Indices: 3624289--3624326 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
3624279 TAGTTTCTAG
3624289 CAGCCACAATA-AC
1 CAGCCACAATAGAC
*
3624302 CAGGCCACAATAGCC
1 CA-GCCACAATAGAC
3624317 CAGCCACAAT
1 CAGCCACAAT
3624327 CAAAAACATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 2 0.09
14 17 0.77
15 3 0.14
ACGTcount: A:0.39, C:0.39, G:0.13, T:0.08
Consensus pattern (14 bp):
CAGCCACAATAGAC
Found at i:3624605 original size:52 final size:53
Alignment explanation
Indices: 3624544--3624685 Score: 193
Period size: 50 Copynumber: 2.8 Consensus size: 53
3624534 TGGCTAGCAT
* * *
3624544 TAGAGAGAGAATGAGTGAAAAAGGGGAAATCCGTTCTTTGGGGTGGCCGCCGG
1 TAGAGAGAGAGTGAGTGAAAAAGGGGAGATCCGATCTTTGGGGTGGCCGCCGG
* * * *
3624597 TA-AGAGAGAGTGAGTGAAAGA-GGGAGATCCAAT-TTT-GGGTGGCCGGCGT
1 TAGAGAGAGAGTGAGTGAAAAAGGGGAGATCCGATCTTTGGGGTGGCCGCCGG
3624646 TAGAGAGAGAGTGAGTGAAAAAGGGGAGATCCGATCTTTG
1 TAGAGAGAGAGTGAGTGAAAAAGGGGAGATCCGATCTTTG
3624686 AGAGAGCCGA
Statistics
Matches: 76, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
49 13 0.17
50 21 0.28
51 20 0.26
52 20 0.26
53 2 0.03
ACGTcount: A:0.30, C:0.11, G:0.39, T:0.20
Consensus pattern (53 bp):
TAGAGAGAGAGTGAGTGAAAAAGGGGAGATCCGATCTTTGGGGTGGCCGCCGG
Found at i:3625622 original size:20 final size:20
Alignment explanation
Indices: 3625597--3625636 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3625587 AAAATCATTT
3625597 TAAAAAAAG-TAATAAATAAA
1 TAAAAAAAGATAA-AAATAAA
*
3625617 TAAAAATAGATAAAAATAAA
1 TAAAAAAAGATAAAAATAAA
3625637 AATAATAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (20 bp):
TAAAAAAAGATAAAAATAAA
Found at i:3625633 original size:16 final size:15
Alignment explanation
Indices: 3625600--3625644 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 15
3625590 ATCATTTTAA
3625600 AAAAAGTAATAAATAAAT
1 AAAAA-TAAT-AA-AAAT
3625618 AAAAATAGATAAAAAT
1 AAAAATA-ATAAAAAT
3625634 AAAAATAATAA
1 AAAAATAATAA
3625645 TGATAATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 4 0.15
16 11 0.42
17 4 0.15
18 7 0.27
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (15 bp):
AAAAATAATAAAAAT
Found at i:3625650 original size:15 final size:16
Alignment explanation
Indices: 3625614--3625644 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3625604 AGTAATAAAT
3625614 AAATAAAAATAGATAA
1 AAATAAAAATAGATAA
3625630 AAATAAAAATA-ATAA
1 AAATAAAAATAGATAA
3625645 TGATAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (16 bp):
AAATAAAAATAGATAA
Found at i:3626129 original size:22 final size:23
Alignment explanation
Indices: 3626101--3626144 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
3626091 TTAGAATAAA
3626101 AAAGGATACAA-AAAAATAAAAC
1 AAAGGATACAATAAAAATAAAAC
* *
3626123 AAAGGATATAATAATAATAAAA
1 AAAGGATACAATAAAAATAAAA
3626145 AAATATAATG
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:0.70, C:0.05, G:0.09, T:0.16
Consensus pattern (23 bp):
AAAGGATACAATAAAAATAAAAC
Found at i:3638058 original size:20 final size:20
Alignment explanation
Indices: 3638033--3638074 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
3638023 TTAATTGGAA
3638033 AACATAATATTTTATAATTT
1 AACATAATATTTTATAATTT
3638053 AACATAATATTTTATAATTT
1 AACATAATATTTTATAATTT
3638073 AA
1 AA
3638075 ACTCACCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (20 bp):
AACATAATATTTTATAATTT
Found at i:3640413 original size:12 final size:13
Alignment explanation
Indices: 3640404--3640433 Score: 51
Period size: 13 Copynumber: 2.2 Consensus size: 13
3640394 ATCCAAAATA
3640404 AAAAAAAAAAGAG
1 AAAAAAAAAAGAG
3640417 AAAAAAAAAGAGAG
1 AAAAAAAAA-AGAG
3640431 AAA
1 AAA
3640434 GCCCTAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGAG
Found at i:3640420 original size:14 final size:14
Alignment explanation
Indices: 3640403--3640433 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3640393 AATCCAAAAT
3640403 AAAAAAAAAAAGAG
1 AAAAAAAAAAAGAG
*
3640417 AAAAAAAAAGAGAG
1 AAAAAAAAAAAGAG
3640431 AAA
1 AAA
3640434 GCCCTAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGAG
Found at i:3641298 original size:19 final size:19
Alignment explanation
Indices: 3641274--3641310 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3641264 CTCCCTAGCT
*
3641274 CCCCAAGAAAGGGGAGCAC
1 CCCCAAGAAAGGGAAGCAC
3641293 CCCCAAGAAAGGGAAGCA
1 CCCCAAGAAAGGGAAGCA
3641311 TTGGTCAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.30, G:0.30, T:0.00
Consensus pattern (19 bp):
CCCCAAGAAAGGGAAGCAC
Found at i:3641617 original size:2 final size:2
Alignment explanation
Indices: 3641608--3641644 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
3641598 ATATATTAAA
*
3641608 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3641645 GTAATTCACT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3644051 original size:22 final size:22
Alignment explanation
Indices: 3644026--3644075 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
3644016 AAAATTTAAG
3644026 TGCTACAATAATTCTGAACACT
1 TGCTACAATAATTCTGAACACT
*
3644048 TGCTATAATAATTCTGAACACT
1 TGCTACAATAATTCTGAACACT
3644070 TGCTAC
1 TGCTAC
3644076 TTTCAGTGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (22 bp):
TGCTACAATAATTCTGAACACT
Found at i:3652543 original size:50 final size:50
Alignment explanation
Indices: 3652489--3652592 Score: 181
Period size: 50 Copynumber: 2.1 Consensus size: 50
3652479 TTCAAATCTC
3652489 ATTAAAAATAAGCAAGAGAGAGATAAAAATTTAGATTATATGTGAATTCA
1 ATTAAAAATAAGCAAGAGAGAGATAAAAATTTAGATTATATGTGAATTCA
** *
3652539 ATTAAAAATAAGCAAGTTAGAGATAAAAATTTAGATTATATGTGAGTTCA
1 ATTAAAAATAAGCAAGAGAGAGATAAAAATTTAGATTATATGTGAATTCA
3652589 ATTA
1 ATTA
3652593 CAATCTTAGA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.50, C:0.04, G:0.15, T:0.31
Consensus pattern (50 bp):
ATTAAAAATAAGCAAGAGAGAGATAAAAATTTAGATTATATGTGAATTCA
Found at i:3653229 original size:20 final size:17
Alignment explanation
Indices: 3653205--3653251 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 17
3653195 AAGAAATAAC
3653205 ATAAAAATAAAATAACTT
1 ATAAAAATAAAATAA-TT
*
3653223 ACTTAAAAATAAACTAATT
1 A--TAAAAATAAAATAATT
3653242 ATAAAAATAA
1 ATAAAAATAA
3653252 TTAAAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 9 0.35
18 1 0.04
19 3 0.12
20 13 0.50
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (17 bp):
ATAAAAATAAAATAATT
Found at i:3653266 original size:20 final size:21
Alignment explanation
Indices: 3653241--3653279 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3653231 ATAAACTAAT
3653241 TATAAA-AATAATTAAAAATA
1 TATAAATAATAATTAAAAATA
*
3653261 TATAAATTATAATTAAAAA
1 TATAAATAATAATTAAAAA
3653280 ATAAGGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
TATAAATAATAATTAAAAATA
Found at i:3661452 original size:11 final size:11
Alignment explanation
Indices: 3661417--3661455 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
3661407 AGTTTTTGAG
3661417 TTTAAAGCT-T
1 TTTAAAGCTGT
*
3661427 GTTTAAAGTTGT
1 -TTTAAAGCTGT
3661439 TTTAAAGCTGT
1 TTTAAAGCTGT
3661450 TTTAAA
1 TTTAAA
3661456 ATTTACAGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 24 0.96
12 1 0.04
ACGTcount: A:0.31, C:0.05, G:0.15, T:0.49
Consensus pattern (11 bp):
TTTAAAGCTGT
Found at i:3661520 original size:5 final size:5
Alignment explanation
Indices: 3661487--3661519 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
3661477 CCAAGTCCAA
*
3661487 TTAAG TTAAG TTAAG TTAAG TTAAG TTAGG TTA
1 TTAAG TTAAG TTAAG TTAAG TTAAG TTAAG TTA
3661520 GATTGAATAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.42
Consensus pattern (5 bp):
TTAAG
Found at i:3662704 original size:108 final size:107
Alignment explanation
Indices: 3662515--3662731 Score: 371
Period size: 108 Copynumber: 2.0 Consensus size: 107
3662505 GTTATAAATG
* * *
3662515 ACATTCGGAATGGATAATTTGATTACGTTAATGATTGTAATTTAGGCATGAAGGGGATTATTCAG
1 ACATTCGGAATGGATAATGTGATTAAGTTAATGATTGTAATTTAAGCATGAAGGGGATTATTCAG
** *
3662580 TGATGTTATGACACTATGAGGTAATAGTTGGGCACAAATATA
66 TGATGCCATGACACTATGAGGTAATAATTGGGCACAAATATA
3662622 NACATTCGGAATGGATAATGTGATTAAGTTAATGATTGTAATTTAAGCATGAAGGGGATTATTCA
1 -ACATTCGGAATGGATAATGTGATTAAGTTAATGATTGTAATTTAAGCATGAAGGGGATTATTCA
3662687 GTGATGCCATGACACTATGAGGTAATAATTGGGCACAAATATA
65 GTGATGCCATGACACTATGAGGTAATAATTGGGCACAAATATA
3662730 AC
1 AC
3662732 CCAATGAAGT
Statistics
Matches: 103, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
107 2 0.02
108 101 0.98
ACGTcount: A:0.35, C:0.09, G:0.24, T:0.32
Consensus pattern (107 bp):
ACATTCGGAATGGATAATGTGATTAAGTTAATGATTGTAATTTAAGCATGAAGGGGATTATTCAG
TGATGCCATGACACTATGAGGTAATAATTGGGCACAAATATA
Found at i:3666069 original size:16 final size:17
Alignment explanation
Indices: 3666019--3666071 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 17
3666009 AGGGAGTGTA
*
3666019 AAAG-AGAAACCAAAGAAC
1 AAAGAAGAAA-CAAAG-AG
*
3666037 AAAGAAGAAACAGAGAG
1 AAAGAAGAAACAAAGAG
3666054 AAAGAA-AAACAAAGAG
1 AAAGAAGAAACAAAGAG
3666070 AA
1 AA
3666072 TACCGTGCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
16 11 0.35
17 7 0.23
18 8 0.26
19 5 0.16
ACGTcount: A:0.70, C:0.09, G:0.21, T:0.00
Consensus pattern (17 bp):
AAAGAAGAAACAAAGAG
Found at i:3666193 original size:34 final size:34
Alignment explanation
Indices: 3666152--3666219 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
3666142 GAAGGAAAAG
3666152 AGAGCCATTTAAGGGCTGATTTTGGAGGCTGAAA
1 AGAGCCATTTAAGGGCTGATTTTGGAGGCTGAAA
**** *
3666186 AGAGCCATTTTTTTGCTGGTTTTGGAGGCTGAAA
1 AGAGCCATTTAAGGGCTGATTTTGGAGGCTGAAA
3666220 GTGTCACTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.25, C:0.12, G:0.31, T:0.32
Consensus pattern (34 bp):
AGAGCCATTTAAGGGCTGATTTTGGAGGCTGAAA
Found at i:3666236 original size:33 final size:34
Alignment explanation
Indices: 3666166--3666247 Score: 121
Period size: 33 Copynumber: 2.4 Consensus size: 34
3666156 CCATTTAAGG
* *
3666166 GCTGATTTTGGAGGCTGAAAAGAGCCATTTTTTT
1 GCTGGTTTTGGAGGCTGAAAAGAGCCACTTTTTT
* *
3666200 GCTGGTTTTGGAGGCTG-AAAGTGTCACTTTTTT
1 GCTGGTTTTGGAGGCTGAAAAGAGCCACTTTTTT
3666233 GCTGGTTTTGGAGGC
1 GCTGGTTTTGGAGGC
3666248 CAAAAAGTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 28 0.64
34 16 0.36
ACGTcount: A:0.17, C:0.12, G:0.32, T:0.39
Consensus pattern (34 bp):
GCTGGTTTTGGAGGCTGAAAAGAGCCACTTTTTT
Found at i:3666255 original size:34 final size:34
Alignment explanation
Indices: 3666166--3666257 Score: 105
Period size: 33 Copynumber: 2.7 Consensus size: 34
3666156 CCATTTAAGG
* ** * * *
3666166 GCTGATTTTGGAGGCTGAAAAGAGCCATTTTTTT
1 GCTGGTTTTGGAGGCCAAAAAGTGTCACTTTTTT
**
3666200 GCTGGTTTTGGAGG-CTGAAAGTGTCACTTTTTT
1 GCTGGTTTTGGAGGCCAAAAAGTGTCACTTTTTT
3666233 GCTGGTTTTGGAGGCCAAAAAGTGT
1 GCTGGTTTTGGAGGCCAAAAAGTGT
3666258 AAAATTTTGC
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
33 27 0.56
34 21 0.44
ACGTcount: A:0.21, C:0.12, G:0.30, T:0.37
Consensus pattern (34 bp):
GCTGGTTTTGGAGGCCAAAAAGTGTCACTTTTTT
Found at i:3666266 original size:33 final size:33
Alignment explanation
Indices: 3666196--3666267 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
3666186 AGAGCCATTT
** ***
3666196 TTTTGCTGGTTTTGGAGGCTGAAAGTGTCACTT
1 TTTTGCTGGTTTTGGAGGCAAAAAGTGTCAAAA
3666229 TTTTGCTGGTTTTGGAGGCCAAAAAGTGT-AAAA
1 TTTTGCTGGTTTTGGAGG-CAAAAAGTGTCAAAA
3666262 TTTTGC
1 TTTTGC
3666268 ATCAGAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
33 25 0.76
34 8 0.24
ACGTcount: A:0.21, C:0.11, G:0.28, T:0.40
Consensus pattern (33 bp):
TTTTGCTGGTTTTGGAGGCAAAAAGTGTCAAAA
Found at i:3666662 original size:25 final size:25
Alignment explanation
Indices: 3666615--3666676 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
3666605 CCCAACAAGC
* * *
3666615 AAGAAA-AATGGACATGGTGCAATA
1 AAGAAAGAATGGGCAAGGTCCAATA
*
3666639 AAGAAAGAATGGGCAAGGTCCAATT
1 AAGAAAGAATGGGCAAGGTCCAATA
3666664 AA-AAAGAAATGGG
1 AAGAAAG-AATGGG
3666677 ATAAGTCCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 10 0.31
25 22 0.69
ACGTcount: A:0.50, C:0.08, G:0.27, T:0.15
Consensus pattern (25 bp):
AAGAAAGAATGGGCAAGGTCCAATA
Found at i:3671093 original size:7 final size:7
Alignment explanation
Indices: 3671081--3671130 Score: 52
Period size: 7 Copynumber: 7.3 Consensus size: 7
3671071 GCAACTTAAG
3671081 AAATACA
1 AAATACA
3671088 AAATACA
1 AAATACA
3671095 AACATATC-
1 AA-ATA-CA
*
3671103 ACA--CA
1 AAATACA
3671108 AAATACA
1 AAATACA
3671115 AAATACA
1 AAATACA
3671122 AAATACA
1 AAATACA
3671129 AA
1 AA
3671131 CTTAAGAAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
4 1 0.03
5 2 0.06
7 28 0.78
8 4 0.11
9 1 0.03
ACGTcount: A:0.68, C:0.18, G:0.00, T:0.14
Consensus pattern (7 bp):
AAATACA
Found at i:3672257 original size:2 final size:2
Alignment explanation
Indices: 3672252--3672289 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3672242 CTTAAGTTCA
3672252 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
3672290 GGAATTTTGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3675400 original size:27 final size:27
Alignment explanation
Indices: 3675319--3675393 Score: 132
Period size: 27 Copynumber: 2.8 Consensus size: 27
3675309 ATAAACTAAA
3675319 CTACATAATAATAATTTTATTCTATTC
1 CTACATAATAATAATTTTATTCTATTC
3675346 CTACATAATAATAATTTTATTCTATTC
1 CTACATAATAATAATTTTATTCTATTC
* *
3675373 CTACAAAATAATTATTTTATT
1 CTACATAATAATAATTTTATT
3675394 TAATTCCATA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (27 bp):
CTACATAATAATAATTTTATTCTATTC
Found at i:3689500 original size:111 final size:108
Alignment explanation
Indices: 3689318--3689526 Score: 310
Period size: 111 Copynumber: 1.9 Consensus size: 108
3689308 TTATACATAA
* * *
3689318 GCTAAAAGAAATTGAAACAAACTATCTAATCATCATCAAAATATAAGAATTAAGACTAATTCTCA
1 GCTAAAAGAAATTGAAACAAACTATCAAATCATCATCAAAATATAAGAATCAAGACTAATTCCCA
*
3689383 TTCATGTTTACAATAAAAAAATGTTAACAAAAACAATGAATCCAT
66 TACATGTTTACAAT-AAAAAA-GTTAACAAAAACAATGAATCCAT
* * *
3689428 GCTAAAAGAAATTGAAACACACTATCAAAATTATCATCAAAATGTAAGAATCAAGACTAATTCCC
1 GCTAAAAGAAATTGAAACAAACTATC-AAATCATCATCAAAATATAAGAATCAAGACTAATTCCC
**
3689493 ATACATGTTTACAATAAATTAGTTAACAAAAACA
65 ATACATGTTTACAATAAAAAAGTTAACAAAAACA
3689527 TGTGATTCTA
Statistics
Matches: 89, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
109 13 0.15
110 29 0.33
111 47 0.53
ACGTcount: A:0.51, C:0.15, G:0.08, T:0.26
Consensus pattern (108 bp):
GCTAAAAGAAATTGAAACAAACTATCAAATCATCATCAAAATATAAGAATCAAGACTAATTCCCA
TACATGTTTACAATAAAAAAGTTAACAAAAACAATGAATCCAT
Found at i:3689715 original size:43 final size:42
Alignment explanation
Indices: 3689667--3689750 Score: 132
Period size: 43 Copynumber: 2.0 Consensus size: 42
3689657 CATATATATA
*
3689667 TAACATCATTAATCACTTTCAAAATAAGCAAACTCATGTTCNC
1 TAACATCATTAATCACTTCCAAAATAAGCAAACTCATGTTC-C
* *
3689710 TAACATCATTAATCGCTTCCAGAATAAGCAAACTCATGTTC
1 TAACATCATTAATCACTTCCAAAATAAGCAAACTCATGTTC
3689751 TTCATGGACT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.38, C:0.24, G:0.07, T:0.30
Consensus pattern (42 bp):
TAACATCATTAATCACTTCCAAAATAAGCAAACTCATGTTCC
Found at i:3692868 original size:4 final size:4
Alignment explanation
Indices: 3692859--3692895 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
3692849 CTATGAGGAG
*
3692859 AAGA AAG- AA-A AAGA AAGA AAGA AAGA AAGA AAAA AAG
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAG
3692896 CTTGGTTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 4 0.14
4 25 0.86
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:3700937 original size:39 final size:39
Alignment explanation
Indices: 3700890--3701060 Score: 195
Period size: 39 Copynumber: 4.5 Consensus size: 39
3700880 GTAGTGTGCA
*
3700890 GTGTGGGAGAGCACATGATGATGATATATGTCATGTCCG
1 GTGTGGGAGAGCACATGATGATGATATATGCCATGTCCG
* *
3700929 GTGTGGGAGAGTACATGATGAAGATATATGCCATGTCCG
1 GTGTGGGAGAGCACATGATGATGATATATGCCATGTCCG
* * * **
3700968 GTGTGGGAGAGCACATGCTGATCATATATGCCTTGTGAG
1 GTGTGGGAGAGCACATGATGATGATATATGCCATGTCCG
* * * **
3701007 GTGTGGGAGTGCACATGAGGAT-AT-TA-GCTATGTGTG
1 GTGTGGGAGAGCACATGATGATGATATATGCCATGTCCG
*
3701043 GTGTGGGAGTGCACATGA
1 GTGTGGGAGAGCACATGA
3701061 GTTGANAAGT
Statistics
Matches: 116, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
36 25 0.22
37 2 0.02
38 2 0.02
39 87 0.75
ACGTcount: A:0.25, C:0.12, G:0.36, T:0.27
Consensus pattern (39 bp):
GTGTGGGAGAGCACATGATGATGATATATGCCATGTCCG
Found at i:3707901 original size:2 final size:2
Alignment explanation
Indices: 3707894--3707932 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3707884 AATAATTTTC
3707894 AT AT AT AT AT 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 AT AT AT AT AT A
3707933 NNNNNNNNNN
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3708005 original size:2 final size:2
Alignment explanation
Indices: 3708000--3708041 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3707990 AAAAAATTTT
3708000 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3708042 ATTTTTTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3718814 original size:25 final size:26
Alignment explanation
Indices: 3718778--3718826 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
3718768 TTAACAACTC
*
3718778 ATATAAATAAATT-ACAAATTTAAGT
1 ATATAAAAAAATTAACAAATTTAAGT
*
3718803 ATATAAAAAAATTAACATATTTAA
1 ATATAAAAAAATTAACAAATTTAA
3718827 TAATCTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (26 bp):
ATATAAAAAAATTAACAAATTTAAGT
Found at i:3721023 original size:24 final size:22
Alignment explanation
Indices: 3720991--3721035 Score: 72
Period size: 24 Copynumber: 2.0 Consensus size: 22
3720981 TTACACAAGC
3720991 TAAAAAGGAGAAATGAAAAGAAAG
1 TAAAAAGGAGAAA--AAAAGAAAG
3721015 TAAAAAGGAGAAAAAAAGAAA
1 TAAAAAGGAGAAAAAAAGAAA
3721036 AAAAAAACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.38
24 13 0.62
ACGTcount: A:0.71, C:0.00, G:0.22, T:0.07
Consensus pattern (22 bp):
TAAAAAGGAGAAAAAAAGAAAG
Found at i:3721723 original size:13 final size:14
Alignment explanation
Indices: 3721707--3721735 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3721697 AATTAATAAA
3721707 TTACTTT-AAATAT
1 TTACTTTAAAATAT
3721720 TTACTTTAAAATAT
1 TTACTTTAAAATAT
3721734 TT
1 TT
3721736 TTTATTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
TTACTTTAAAATAT
Found at i:3724442 original size:27 final size:27
Alignment explanation
Indices: 3724411--3724466 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
3724401 AACAATTAAC
*
3724411 TATATTCATTAATTAAATATTAAGTCT
1 TATATTCATTAATTAAATAATAAGTCT
*
3724438 TATATTCATTAATTAAATAATAATTCT
1 TATATTCATTAATTAAATAATAAGTCT
3724465 TA
1 TA
3724467 CTTTTTATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (27 bp):
TATATTCATTAATTAAATAATAAGTCT
Found at i:3725888 original size:20 final size:20
Alignment explanation
Indices: 3725852--3725889 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3725842 ACAAAGAAAC
*
3725852 TTTTTAACTTTTAACTTTAG
1 TTTTTAACCTTTAACTTTAG
3725872 TTTTTCAACCTTT-ACTTT
1 TTTTT-AACCTTTAACTTT
3725890 TGGATATTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.21, C:0.16, G:0.03, T:0.61
Consensus pattern (20 bp):
TTTTTAACCTTTAACTTTAG
Found at i:3726421 original size:28 final size:28
Alignment explanation
Indices: 3726363--3726421 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
3726353 ACATTTCATT
*
3726363 TTCTATTATATCTCGATGAATAACTCAA
1 TTCTATTATATCTCGATGAATAACCCAA
*
3726391 TTCTATTATATC-CTGATGAATAACCCGA
1 TTCTATTATATCTC-GATGAATAACCCAA
3726419 TTC
1 TTC
3726422 CTCATATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 1 0.04
28 27 0.96
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.39
Consensus pattern (28 bp):
TTCTATTATATCTCGATGAATAACCCAA
Found at i:3747264 original size:15 final size:15
Alignment explanation
Indices: 3747231--3747286 Score: 60
Period size: 15 Copynumber: 3.8 Consensus size: 15
3747221 ACTTTATAAT
* *
3747231 GTAATATGATTACAG
1 GTAATATGATTGCAA
3747246 GTAATATGATTGCAA
1 GTAATATGATTGCAA
*
3747261 GTAATGT-ATTGCAA
1 GTAATATGATTGCAA
* *
3747275 GCAATGTGATTG
1 GTAATATGATTG
3747287 TAGCGAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
14 13 0.36
15 23 0.64
ACGTcount: A:0.36, C:0.07, G:0.23, T:0.34
Consensus pattern (15 bp):
GTAATATGATTGCAA
Found at i:3747273 original size:14 final size:15
Alignment explanation
Indices: 3747252--3747286 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
3747242 ACAGGTAATA
*
3747252 TGATTGCAAGTAATG
1 TGATTGCAAGCAATG
3747267 T-ATTGCAAGCAATG
1 TGATTGCAAGCAATG
3747281 TGATTG
1 TGATTG
3747287 TAGCGAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (15 bp):
TGATTGCAAGCAATG
Found at i:3747543 original size:20 final size:20
Alignment explanation
Indices: 3747518--3747670 Score: 60
Period size: 20 Copynumber: 7.1 Consensus size: 20
3747508 ATTTTATTTT
3747518 TATTTTTTATTATAATATTA
1 TATTTTTTATTATAATATTA
3747538 TATTTTGATTTTTATTATAATATTA
1 TA---T--TTTTTATTATAATATTA
* *
3747563 TATTTTATTTTAATTTTTTAAATATAA
1 TA--TT-TTTT-A--TTAT-AATATTA
* * *
3747590 TATTTTATATT-TTATTTTA
1 TATTTTTTATTATAATATTA
* * *
3747609 -ATTTTTAATTCTTATATTA
1 TATTTTTTATTATAATATTA
* *
3747628 TATATTTTATTTTAATATT-
1 TATTTTTTATTATAATATTA
*
3747647 TTTTATTTTAATTATAATATTA
1 TATT-TTTT-ATTATAATATTA
3747669 TA
1 TA
3747671 AAATATTTTT
Statistics
Matches: 101, Mismatches: 17, Indels: 28
0.69 0.12 0.19
Matches are distributed among these distances:
18 8 0.08
19 13 0.13
20 21 0.21
21 12 0.12
22 2 0.02
23 6 0.06
24 7 0.07
25 21 0.21
26 3 0.03
27 8 0.08
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (20 bp):
TATTTTTTATTATAATATTA
Found at i:3747549 original size:25 final size:24
Alignment explanation
Indices: 3747511--3747610 Score: 103
Period size: 25 Copynumber: 4.0 Consensus size: 24
3747501 GTCATATATT
3747511 TTAT-TTTTATTTTTTATTATAATA
1 TTATATTTTA-TTTTTATTATAATA
3747535 TTATATTTTGATTTTTATTATAATA
1 TTATATTTT-ATTTTTATTATAATA
* *
3747560 TTATATTTTATTTTAATTTTTTAAATA
1 TTATATTTTATTTT--TATTAT-AATA
* *
3747587 TAATATTTTATATTTTATTTTAAT
1 TTATATTTTAT-TTTTATTATAAT
3747611 TTTTAATTCT
Statistics
Matches: 66, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
24 9 0.14
25 30 0.45
26 10 0.15
27 14 0.21
28 3 0.05
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (24 bp):
TTATATTTTATTTTTATTATAATA
Found at i:3747661 original size:33 final size:34
Alignment explanation
Indices: 3747512--3747667 Score: 125
Period size: 33 Copynumber: 4.7 Consensus size: 34
3747502 TCATATATTT
* *
3747512 TATTTTT-ATTTTTTATTATAATATTATATTTT--
1 TATTTTTAATTTTATATTAT-ATATTTTATTTTAA
* *
3747544 GATTTTT-A--TTATAATATTATATTTTATTTTAA
1 TATTTTTAATTTTATATTA-TATATTTTATTTTAA
* * *
3747576 T-TTTTTAAATATAATATTTTATATTTTATTTT-A
1 TATTTTT-AATTTTATATTATATATTTTATTTTAA
3747609 -ATTTTTAATTCTTATATTATATATTTTATTTTAA
1 TATTTTTAATT-TTATATTATATATTTTATTTTAA
*
3747643 TATTTTTTATTTTA-ATTATAATATT
1 TATTTTTAATTTTATATTAT-ATATT
3747668 ATAAAATATT
Statistics
Matches: 100, Mismatches: 12, Indels: 22
0.75 0.09 0.16
Matches are distributed among these distances:
30 17 0.17
31 6 0.06
32 10 0.10
33 31 0.31
34 22 0.22
35 14 0.14
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.67
Consensus pattern (34 bp):
TATTTTTAATTTTATATTATATATTTTATTTTAA
Found at i:3748542 original size:2 final size:2
Alignment explanation
Indices: 3748537--3748566 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3748527 TTTAACATTC
3748537 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
3748567 TAAAAATGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3748915 original size:24 final size:24
Alignment explanation
Indices: 3748886--3748935 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
3748876 CGACCCATAT
3748886 ATACCTTAAAACCGAAAGCCAGCC
1 ATACCTTAAAACCGAAAGCCAGCC
3748910 ATACCTTAAAACCGAAAGCCAGCC
1 ATACCTTAAAACCGAAAGCCAGCC
3748934 AT
1 AT
3748936 CCAATAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.42, C:0.32, G:0.12, T:0.14
Consensus pattern (24 bp):
ATACCTTAAAACCGAAAGCCAGCC
Found at i:3756026 original size:22 final size:23
Alignment explanation
Indices: 3755968--3756050 Score: 87
Period size: 22 Copynumber: 3.5 Consensus size: 23
3755958 TATTAGATTT
3755968 TTTAAATATTAATAATCTAGAATTTAA
1 TTTAAATATTAATAAT-T--AA-TTAA
*
3755995 TTAAAATATTAATAATTAATT-A
1 TTTAAATATTAATAATTAATTAA
* * *
3756017 TTTAAATATTAACATTTATTTAA
1 TTTAAATATTAATAATTAATTAA
3756040 TTTAAATATTA
1 TTTAAATATTA
3756051 TTATGATTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
22 18 0.36
23 14 0.28
24 2 0.04
26 1 0.02
27 15 0.30
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (23 bp):
TTTAAATATTAATAATTAATTAA
Found at i:3757106 original size:19 final size:20
Alignment explanation
Indices: 3757056--3757114 Score: 75
Period size: 19 Copynumber: 3.0 Consensus size: 20
3757046 CTCTATTCCT
3757056 AGTGTTTCTAACAGATTTCGC
1 AGTGTTTCTAACAGA-TTCGC
* * *
3757077 AGTATTGCTAACAG-TTCGG
1 AGTGTTTCTAACAGATTCGC
3757096 AGTGTTTCTAACAGATTCG
1 AGTGTTTCTAACAGATTCG
3757115 TACCTAGCAG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
19 16 0.50
20 4 0.12
21 12 0.38
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (20 bp):
AGTGTTTCTAACAGATTCGC
Found at i:3771886 original size:27 final size:27
Alignment explanation
Indices: 3771856--3771940 Score: 93
Period size: 27 Copynumber: 3.1 Consensus size: 27
3771846 ACGCACTTAA
*
3771856 GAACGTTCCTATACGTTATGCACTTGG
1 GAACGTTCCTATGCGTTATGCACTTGG
* *
3771883 GAACGTTCCTATGCTTTATGCA-TTAGA
1 GAACGTTCCTATGCGTTATGCACTT-GG
* *
3771910 AAACG-TCCATATGTGTTATGCACTTGG
1 GAACGTTCC-TATGCGTTATGCACTTGG
3771937 GAAC
1 GAAC
3771941 ATCACTTAGG
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
26 5 0.11
27 40 0.85
28 2 0.04
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (27 bp):
GAACGTTCCTATGCGTTATGCACTTGG
Found at i:3774974 original size:28 final size:28
Alignment explanation
Indices: 3774915--3774974 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
3774905 TGGGTGGTGT
* * * *
3774915 AAAATTACAATTTTACCCCTAGAGTGGC
1 AAAATGACAATTTTACCCCTAGACTCGA
* *
3774943 AAAATGACTATTTTACCCCTATACTCGA
1 AAAATGACAATTTTACCCCTAGACTCGA
3774971 AAAA
1 AAAA
3774975 ATATCGAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.28
Consensus pattern (28 bp):
AAAATGACAATTTTACCCCTAGACTCGA
Found at i:3790302 original size:23 final size:23
Alignment explanation
Indices: 3790276--3790371 Score: 66
Period size: 23 Copynumber: 3.8 Consensus size: 23
3790266 ACGCATCATG
3790276 TTCAAAAAATGTTACACGCCACA
1 TTCAAAAAATGTTACACGCCACA
* * *
3790299 TTCACAACATGTTACATGCCATGTGCCA
1 TTCAAAAAATGTTACACGCCA-----CA
**
3790327 TGTTCAAAAAATGTTACACGCCATG
1 --TTCAAAAAATGTTACACGCCACA
3790352 TTCAATAAAAATGTTACACG
1 TTC-A-AAAAATGTTACACG
3790372 TCATGTGCTA
Statistics
Matches: 56, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
23 21 0.38
24 1 0.02
25 14 0.25
28 2 0.04
30 18 0.32
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (23 bp):
TTCAAAAAATGTTACACGCCACA
Found at i:3790376 original size:25 final size:23
Alignment explanation
Indices: 3790323--3790377 Score: 83
Period size: 25 Copynumber: 2.3 Consensus size: 23
3790313 CATGCCATGT
3790323 GCCATGTTCAAAAAATGTTACAC
1 GCCATGTTCAAAAAATGTTACAC
3790346 GCCATGTTCAATAAAAATGTTACAC
1 GCCATGTTC-A-AAAAATGTTACAC
*
3790371 GTCATGT
1 GCCATGT
3790378 GCTAACACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 9 0.31
24 1 0.03
25 19 0.66
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (23 bp):
GCCATGTTCAAAAAATGTTACAC
Found at i:3790772 original size:63 final size:63
Alignment explanation
Indices: 3790613--3790777 Score: 174
Period size: 63 Copynumber: 2.6 Consensus size: 63
3790603 CACGATAACG
* * * *
3790613 ATAGTGCTCAACAGATAGTTGACAGAGCTGATACAATTCAGAGATCTGAGAGACACAATGACA
1 ATAGTGCTCAACAGAGAGTTGACAGAGCTGATACAATTCAAAAATCTGAAAGACACAATGACA
* * * ** *
3790676 AT-GATGCTCAACAAAGAGTTGACAGAGCCGATACAATTCAAAAATTTGAAAGAGC-TGATGATA
1 ATAG-TGCTCAACAGAGAGTTGACAGAGCTGATACAATTCAAAAATCTGAAAGA-CACAATGACA
* * *
3790739 ATAGTGCTCAACAGAGAATTGACATAGTTGATAC-ATTCA
1 ATAGTGCTCAACAGAGAGTTGACAGAGCTGATACAATTCA
3790778 GAGAGTTGAG
Statistics
Matches: 84, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
62 6 0.07
63 76 0.90
64 2 0.02
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.23
Consensus pattern (63 bp):
ATAGTGCTCAACAGAGAGTTGACAGAGCTGATACAATTCAAAAATCTGAAAGACACAATGACA
Found at i:3791815 original size:18 final size:18
Alignment explanation
Indices: 3791779--3791816 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3791769 ATGTAAGATC
*
3791779 ATATTTTATTTAATTCTA
1 ATATTTTATTTAATGCTA
3791797 ATATTTTAGTTT-ATGCTA
1 ATATTTTA-TTTAATGCTA
3791815 AT
1 AT
3791817 GAGTAGTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (18 bp):
ATATTTTATTTAATGCTA
Found at i:3794117 original size:19 final size:19
Alignment explanation
Indices: 3794093--3794132 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
3794083 AATGTAAAGT
3794093 TAAAATGTTATTTGAGAAC
1 TAAAATGTTATTTGAGAAC
3794112 TAAAATGTTATTTGAGAAC
1 TAAAATGTTATTTGAGAAC
3794131 TA
1 TA
3794133 TCTCTTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.38
Consensus pattern (19 bp):
TAAAATGTTATTTGAGAAC
Found at i:3800624 original size:19 final size:20
Alignment explanation
Indices: 3800590--3800635 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
3800580 TTTTGTTTAC
* * *
3800590 TGCCCCCCCTCTCCCCCGCT
1 TGCCCCCCCCCCCCCCCCCT
3800610 T-CCCCCCCCCCCCCCCCCT
1 TGCCCCCCCCCCCCCCCCCT
3800629 TGCCCCC
1 TGCCCCC
3800636 TTTTCTCATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.00, C:0.78, G:0.07, T:0.15
Consensus pattern (20 bp):
TGCCCCCCCCCCCCCCCCCT
Found at i:3810541 original size:23 final size:25
Alignment explanation
Indices: 3810496--3810543 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 25
3810486 CATAATATGA
3810496 TTCATAACATCGAATCTCATTTCAT
1 TTCATAACATCGAATCTCATTTCAT
*
3810521 TTCATAA-ATC-AATTTCATTTCAT
1 TTCATAACATCGAATCTCATTTCAT
3810544 AAAAATCAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 12 0.55
24 3 0.14
25 7 0.32
ACGTcount: A:0.33, C:0.21, G:0.02, T:0.44
Consensus pattern (25 bp):
TTCATAACATCGAATCTCATTTCAT
Found at i:3814255 original size:2 final size:2
Alignment explanation
Indices: 3814250--3814274 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3814240 ATCATCTCTC
3814250 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3814275 GTATGTCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3817694 original size:20 final size:20
Alignment explanation
Indices: 3817671--3817711 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
3817661 ATCGAATCTC
*
3817671 ATTTCATTTCATATAAATCA
1 ATTTCATTTCATAAAAATCA
3817691 ATTTCATTTCATAAAAATCA
1 ATTTCATTTCATAAAAATCA
3817711 A
1 A
3817712 CAAGGCTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (20 bp):
ATTTCATTTCATAAAAATCA
Found at i:3819766 original size:27 final size:26
Alignment explanation
Indices: 3819735--3819800 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 26
3819725 CAACATTCCA
*
3819735 ATTTTGCCCTTAGGTGGCAAAATGACC
1 ATTTT-CCCTTAGATGGCAAAATGACC
3819762 ATTTTACCCTTAGATGGCAAAATGACC
1 ATTTT-CCCTTAGATGGCAAAATGACC
3819789 ATTTATCCCTTA
1 ATTT-TCCCTTA
3819801 CATTATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 35 0.97
28 1 0.03
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (26 bp):
ATTTTCCCTTAGATGGCAAAATGACC
Found at i:3821259 original size:352 final size:351
Alignment explanation
Indices: 3820464--3821337 Score: 1163
Period size: 352 Copynumber: 2.5 Consensus size: 351
3820454 CTTCTCCTTT
* * * * *
3820464 AGATCACCAAGGAG-TTTAATATCCACTATCTCAAAAATTCTTTTTTAGAACAAAGCATAACCCT
1 AGATCACTAAGGAGTTTTGA-ATCCACTATCTAAAAAATGCTTTTCTAGAACAAAGCATAACCCT
* * * *
3820528 CATAATCAG-TCTTTCAAAGGCCTAGACTTAACC-TCTACTTTTTCACTTGGTAAGGAATAACCA
65 CACAATCAGTTTTTTCAAAGGCTTAGACTTAACCTTCTACTTTTTCACTTGGTAAGGTATAACCA
* *
3820591 TTCAACAACAC-TATC-TTTAAAGGTTAAGATAGAACCTTTACAATCAATATAATAAGGATGAAA
130 TTCAACAACACTTATCTTTTCAAGGTTAAGATAGAACCTTTACAATCAATACAATAAGGATGAAA
* ** * * * *
3820654 AAGAAAACTCAAGTGCCTTTACAAGACTGAATAATATAATGAGTTCAAGAAGACTATGAAGGCTC
195 AAGAAAACTCAAATGCCTTTACAAGACCCAATAATACAATGAATACAAGAACACTATGAAGGCTC
* ** * *
3820719 TTGAAAGAATAAGGAAGCTTAAGGCTTTAGTAACTCAATGAAAGAGCATTTTGATTTTGAGAGTA
260 TGGAAAGAATAAGGAAGCTTAAGGCTCAAGTAACTCAATGAAAGAACACTTTGATTTTGAGAGTA
3820784 ATTTTGGAGAAATCTTGAGTTGGCCTC
325 ATTTTGGAGAAATCTTGAGTTGGCCTC
* * * * * *
3820811 ATATCACTAAAGCA-TTTAGGATCCACTATCTAAAAAATGCTTTTCTA-AGACAAAACATAACTC
1 AGATCACT-AAGGAGTTTTGAATCCACTATCTAAAAAATGCTTTTCTAGA-ACAAAGCATAACCC
* * *
3820874 TCACAATTAGTTTTCTT-AAAGGCTTAGACTTAACCTTTTTACTTTTTCACTTGATAAGGTATAA
64 TCACAATCAGTTTT-TTCAAAGGCTTAGACTTAACC-TTCTACTTTTTCACTTGGTAAGGTATAA
* *
3820938 CTATTCAACAACACTTATCTTTTCAAGGTTAAGATAAAACCTTTACAATCAATACAATAAGGATG
127 CCATTCAACAACACTTATCTTTTCAAGGTTAAGATAGAACCTTTACAATCAATACAATAAGGATG
* * * * *
3821003 AAAAAGAAAGCTCAAATGCCTTTAGAAGGCCCAATAATACAATGAATACAAGAACAGTTTGAAGG
192 AAAAAGAAAACTCAAATGCCTTTACAAGACCCAATAATACAATGAATACAAGAACACTATGAAGG
**
3821068 CTCTGGAAAGAATAAGGAAGCTTAAGGCTCAAGTAGGTCAATGAAAGAACACTTTGATTTTGAGA
257 CTCTGGAAAGAATAAGGAAGCTTAAGGCTCAAGTAACTCAATGAAAGAACACTTTGATTTTGAGA
* * *
3821133 GTTATTTTGGAGAAATCTTTAGTTGGCCTT
322 GTAATTTTGGAGAAATCTTGAGTTGGCCTC
* *
3821163 GGATCACTAAGGAGTTTTGAATCCATTATCTAAAAAATGCTTTTCTAGAACAAAGCATAACCCTC
1 AGATCACTAAGGAGTTTTGAATCCACTATCTAAAAAATGCTTTTCTAGAACAAAGCATAACCCTC
* * *
3821228 ACAATCAGTTTTTTCAAAGACTTAAACTTAACCCTTCTACCTTTTCACTTGGTAAGGTATAACCA
66 ACAATCAGTTTTTTCAAAGGCTTAGACTTAA-CCTTCTACTTTTTCACTTGGTAAGGTATAACCA
* * *
3821293 CTCAACAATA-TTATTTTTTCAAGGTTAAGATAGAACCTTTACAAT
130 TTCAACAACACTTATCTTTTCAAGGTTAAGATAGAACCTTTACAAT
3821338 TAACACTTAC
Statistics
Matches: 451, Mismatches: 63, Indels: 22
0.84 0.12 0.04
Matches are distributed among these distances:
346 1 0.00
347 50 0.11
348 25 0.06
349 2 0.00
350 37 0.08
351 43 0.10
352 290 0.64
353 3 0.01
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.31
Consensus pattern (351 bp):
AGATCACTAAGGAGTTTTGAATCCACTATCTAAAAAATGCTTTTCTAGAACAAAGCATAACCCTC
ACAATCAGTTTTTTCAAAGGCTTAGACTTAACCTTCTACTTTTTCACTTGGTAAGGTATAACCAT
TCAACAACACTTATCTTTTCAAGGTTAAGATAGAACCTTTACAATCAATACAATAAGGATGAAAA
AGAAAACTCAAATGCCTTTACAAGACCCAATAATACAATGAATACAAGAACACTATGAAGGCTCT
GGAAAGAATAAGGAAGCTTAAGGCTCAAGTAACTCAATGAAAGAACACTTTGATTTTGAGAGTAA
TTTTGGAGAAATCTTGAGTTGGCCTC
Found at i:3822876 original size:203 final size:204
Alignment explanation
Indices: 3822517--3823126 Score: 988
Period size: 204 Copynumber: 3.0 Consensus size: 204
3822507 GTGAATTTTA
* * *
3822517 TTTTTTACCTTACCTTGACTTAGTCTTTTTACTGTGAAGAAAGAATTAGTCTTTGATTCACATTT
1 TTTTTTGCCTTACCTTGACTTAGTCGTTTTACTGTGAAGAAAGAATTAGTCTTTGATTCACATTC
* * *
3822582 TTCCATTATAAATATTTTGTAACGTTAGACATAATATTTTATCTTGATTTAGTCTTTGATTCTTT
66 TACCATTATAAATATTTTGTAACGTTAGACAAAATATTATATCTTGATTTAGTCTTTGATTCTTT
* *
3822647 TAAGATATTTATAATGTTACAAAATATTTTATCTTGATTTTCTCTTGATTCTCTCAGCCGTTTCT
131 TAAGATATTTATAACGTTATAAAATATTTTATCTTGATTTTCTCTTGATTCTCTCAGCCGTTTCT
3822712 CTCTATAAT
196 CTCTATAAT
* * *
3822721 TTTTTTGCCTTACCTTGGCTTTGTCGTTTTACTATGAAGAAAGAATTAGTCTTTGATTCACATTC
1 TTTTTTGCCTTACCTTGACTTAGTCGTTTTACTGTGAAGAAAGAATTAGTCTTTGATTCACATTC
* *
3822786 TGCCATTATAAATA-TTTGTAACGTTAGACAAAATATTATATCTTGATTTAGTCTTTGAGTCTTT
66 TACCATTATAAATATTTTGTAACGTTAGACAAAATATTATATCTTGATTTAGTCTTTGATTCTTT
* *
3822850 TAAGATATTTATAACGTTATAAAATATTTTATCTTGATTTTCTATTGATTCTCTCAACCGTTTCT
131 TAAGATATTTATAACGTTATAAAATATTTTATCTTGATTTTCTCTTGATTCTCTCAGCCGTTTCT
*
3822915 CTTTATAAT
196 CTCTATAAT
* * *
3822924 TTTTTTGCCTTACCTTAACTTAGTTGTTTTATTGTGAAGAAAGAATTAGTCTTTGATTCACATTC
1 TTTTTTGCCTTACCTTGACTTAGTCGTTTTACTGTGAAGAAAGAATTAGTCTTTGATTCACATTC
** *
3822989 TACTGTTATAAATATTTTGTAACGTTCGACAAAATATTATATCTTGATTTAGTCTTTGATTCTTT
66 TACCATTATAAATATTTTGTAACGTTAGACAAAATATTATATCTTGATTTAGTCTTTGATTCTTT
* *
3823054 TAGGATATTTATAACGTTATAAAATATTTTATCTTGATTTTCTCTTGATTCTCTCAGCCATTTCT
131 TAAGATATTTATAACGTTATAAAATATTTTATCTTGATTTTCTCTTGATTCTCTCAGCCGTTTCT
*
3823119 TTCTATAA
196 CTCTATAA
3823127 ATATAGCCTC
Statistics
Matches: 373, Mismatches: 32, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
203 186 0.50
204 187 0.50
ACGTcount: A:0.27, C:0.14, G:0.11, T:0.49
Consensus pattern (204 bp):
TTTTTTGCCTTACCTTGACTTAGTCGTTTTACTGTGAAGAAAGAATTAGTCTTTGATTCACATTC
TACCATTATAAATATTTTGTAACGTTAGACAAAATATTATATCTTGATTTAGTCTTTGATTCTTT
TAAGATATTTATAACGTTATAAAATATTTTATCTTGATTTTCTCTTGATTCTCTCAGCCGTTTCT
CTCTATAAT
Found at i:3823095 original size:204 final size:204
Alignment explanation
Indices: 3822517--3823126 Score: 974
Period size: 203 Copynumber: 3.0 Consensus size: 204
3822507 GTGAATTTTA
*
3822517 TTTTTTACCTTACCTTGACTTAGTCT-TTTTACTGTGAAGAAAGAATTAGTCTTTGATTCACATT
1 TTTTTTGCCTTACCTTGACTTAGT-TGTTTTACTGTGAAGAAAGAATTAGTCTTTGATTCACATT
* * * *
3822581 TTTCCATTATAAATATTTTGTAACGTTAGACATAATATTTTATCTTGATTTAGTCTTTGATTCTT
65 CTACCATTATAAATATTTTGTAACGTTAGACAAAATATTATATCTTGATTTAGTCTTTGATTCTT
* *
3822646 TTAAGATATTTATAATGTTACAAAATATTTTATCTTGATTTTCTCTTGATTCTCTCAGCCGTTTC
130 TTAAGATATTTATAACGTTATAAAATATTTTATCTTGATTTTCTCTTGATTCTCTCAGCCGTTTC
*
3822711 TCTCTATAAT
195 TCTTTATAAT
* * * *
3822721 TTTTTTGCCTTACCTTGGCTTTGTCGTTTTACTATGAAGAAAGAATTAGTCTTTGATTCACATTC
1 TTTTTTGCCTTACCTTGACTTAGTTGTTTTACTGTGAAGAAAGAATTAGTCTTTGATTCACATTC
* *
3822786 TGCCATTATAAATA-TTTGTAACGTTAGACAAAATATTATATCTTGATTTAGTCTTTGAGTCTTT
66 TACCATTATAAATATTTTGTAACGTTAGACAAAATATTATATCTTGATTTAGTCTTTGATTCTTT
* *
3822850 TAAGATATTTATAACGTTATAAAATATTTTATCTTGATTTTCTATTGATTCTCTCAACCGTTTCT
131 TAAGATATTTATAACGTTATAAAATATTTTATCTTGATTTTCTCTTGATTCTCTCAGCCGTTTCT
3822915 CTTTATAAT
196 CTTTATAAT
* *
3822924 TTTTTTGCCTTACCTTAACTTAGTTGTTTTATTGTGAAGAAAGAATTAGTCTTTGATTCACATTC
1 TTTTTTGCCTTACCTTGACTTAGTTGTTTTACTGTGAAGAAAGAATTAGTCTTTGATTCACATTC
** *
3822989 TACTGTTATAAATATTTTGTAACGTTCGACAAAATATTATATCTTGATTTAGTCTTTGATTCTTT
66 TACCATTATAAATATTTTGTAACGTTAGACAAAATATTATATCTTGATTTAGTCTTTGATTCTTT
* *
3823054 TAGGATATTTATAACGTTATAAAATATTTTATCTTGATTTTCTCTTGATTCTCTCAGCCATTTCT
131 TAAGATATTTATAACGTTATAAAATATTTTATCTTGATTTTCTCTTGATTCTCTCAGCCGTTTCT
3823119 -TTCTATAA
196 CTT-TATAA
3823127 ATATAGCCTC
Statistics
Matches: 373, Mismatches: 30, Indels: 6
0.91 0.07 0.01
Matches are distributed among these distances:
203 188 0.50
204 185 0.50
ACGTcount: A:0.27, C:0.14, G:0.11, T:0.49
Consensus pattern (204 bp):
TTTTTTGCCTTACCTTGACTTAGTTGTTTTACTGTGAAGAAAGAATTAGTCTTTGATTCACATTC
TACCATTATAAATATTTTGTAACGTTAGACAAAATATTATATCTTGATTTAGTCTTTGATTCTTT
TAAGATATTTATAACGTTATAAAATATTTTATCTTGATTTTCTCTTGATTCTCTCAGCCGTTTCT
CTTTATAAT
Found at i:3860340 original size:250 final size:249
Alignment explanation
Indices: 3859827--3860876 Score: 1060
Period size: 250 Copynumber: 4.2 Consensus size: 249
3859817 GGGTCGTGAC
* * *
3859827 ACATTGTCAAAATATTAATGT-AA-GTGTGAGATTTAACGTAACATA-TCAATTATATCAAATAA
1 ACATTGTC-AAATATTGATGTAAATGTGTGAGATTTAACGTAACA-AGTTAATTATGTCAAATAA
* ** * *
3859889 ATATAATCTTCAGGAAAATTAAACATTTAAATTTTTATTCTTGAGTTTAAAGTGTTTTATGGCTT
64 ACATAAT-TTTTGGAAAATTAAACATTTAAATTTTTATTCTCGAGTTTAAAGTATTTTATGGCTT
** * * * *
3859954 ACAAATTTTGTTCTATGTATGAATAATAGTAAGGAT-AAAATAATTACAGTGAAAATTAATAGTT
128 ACAAATTTTAATCTATGAATGAATAATAGTAAAGATAAAAATAATTATAGTGAAAATTAGTAGTT
* ** * * * * *
3860018 G-AAAACGTTGACGTAAAACAATAAAAATTAATATAAAAAATTGTAAAGGTGGAATAG
193 GAAAAACGTTGACGTAAAAC-GTAAAAATTAACGTAAAAAATTATAAAAGTAGAAAAA
* * * * * *
3860075 ACATTGTTAAAATATTAACGTAAATATGTGAGATTTAACGTAACAAGTTTATTACGTCAAATAAA
1 ACATTG-TCAAATATTGATGTAAATGTGTGAGATTTAACGTAACAAGTTAATTATGTCAAATAAA
* *
3860140 CATAATTTTTGAGAAAATTAAACATTTAACTCTTTACTT-TCGAGTTTAAAGTATTTTATGG-TG
65 CATAATTTTTG-GAAAATTAAACATTTAAATTTTTA-TTCTCGAGTTTAAAGTATTTTATGGCT-
* * * * * * *
3860203 TATAAATTTTAATTTGTGGATGAAGAATAGTAAGGAT-AAAATAATTATAGT-ATTAATTAGTAG
127 TACAAATTTTAATCTATGAATGAATAATAGTAAAGATAAAAATAATTATAGTGA-AAATTAGTAG
* * * ** * *
3860266 TTGAATAACTTTTACGTAAAGTGATAAGAATTAACGTAAAATATTATAAAAGTAGAAAAA
191 TTGAAAAACGTTGACGTAAAACG-TAAAAATTAACGTAAAAAATTATAAAAGTAGAAAAA
* * * * * *
3860326 AAATTGTCAAATATTGATGTAAATGTGTAAGATTTAATGTAACAAGTAAATTATGTCAAACAAAA
1 ACATTGTCAAATATTGATGTAAATGTGTGAGATTTAACGTAACAAGTTAATTATGTCAAATAAAC
* * * * *
3860391 ATAATTTTTGGAGAAATTCAACATTTAAATTGTTATTCTCGAATTTAAAGTGTTTTACGGCTTAC
66 ATAATTTTTGGA-AAATTAAACATTTAAATTTTTATTCTCGAGTTTAAAGTATTTTATGGCTTAC
*
3860456 AAATTTTAATCTAT-ACATGAATAATAATAAAGATAAAAATAATTATAGTGAAAATTAGTAGTTG
130 AAATTTTAATCTATGA-ATGAATAATAGTAAAGATAAAAATAATTATAGTGAAAATTAGTAGTTG
* * * * * *
3860520 AAAAACGTTAACATAAGACCGTAAAAATTAACGTAATAAATTATAAAGGTAGAATAA
194 AAAAACGTTGACGTAA-AACGTAAAAATTAACGTAAAAAATTATAAAAGTAGAAAAA
* * * * * * *
3860577 GCATTGTCAAAATATTGATATAAATATGTTAGATTTAATGTAATAAGTTAGTTATGTCAAATAAA
1 ACATTGTC-AAATATTGATGTAAATGTGTGAGATTTAACGTAACAAGTTAATTATGTCAAATAAA
* * * *
3860642 CATAATTTTTTGGAAAATTAAACATTTAGATTTTTATTTTCAAGTTTAAAGTATTTTGTGGCTTA
65 CATAA-TTTTTGGAAAATTAAACATTTAAATTTTTATTCTCGAGTTTAAAGTATTTTATGGCTTA
* * * * * * *
3860707 TAAGTTTTAATCTATGAATGGATAATAGTAAAGATAAAAATAATTATTGTGAAAGTTAGTACTTA
129 CAAATTTTAATCTATGAATGAATAATAGTAAAGATAAAAATAATTATAGTGAAAATTAGTAGTTG
* * * * *
3860772 AAAAACCTTGACGCAAAATTGTAAAAATTAACGTAAAAAATTATGAAAGTAGACAAA
194 AAAAACGTTGACGTAAAA-CGTAAAAATTAACGTAAAAAATTATAAAAGTAGAAAAA
** * *
3860829 GTATTGTAAAAATATTGACGT-AATCGTGTGAGATTTAACGTAACAAGT
1 ACATTGT-CAAATATTGATGTAAAT-GTGTGAGATTTAACGTAACAAGT
3860877 AATAATAATA
Statistics
Matches: 656, Mismatches: 123, Indels: 42
0.80 0.15 0.05
Matches are distributed among these distances:
248 17 0.03
249 13 0.02
250 258 0.39
251 127 0.19
252 232 0.35
253 9 0.01
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.35
Consensus pattern (249 bp):
ACATTGTCAAATATTGATGTAAATGTGTGAGATTTAACGTAACAAGTTAATTATGTCAAATAAAC
ATAATTTTTGGAAAATTAAACATTTAAATTTTTATTCTCGAGTTTAAAGTATTTTATGGCTTACA
AATTTTAATCTATGAATGAATAATAGTAAAGATAAAAATAATTATAGTGAAAATTAGTAGTTGAA
AAACGTTGACGTAAAACGTAAAAATTAACGTAAAAAATTATAAAAGTAGAAAAA
Found at i:3870757 original size:13 final size:13
Alignment explanation
Indices: 3870739--3870763 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3870729 GGAAAATGAG
3870739 ATTTTATAAAATA
1 ATTTTATAAAATA
3870752 ATTTTATAAAAT
1 ATTTTATAAAAT
3870764 TTTTGAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTATAAAATA
Found at i:3871671 original size:2 final size:2
Alignment explanation
Indices: 3871664--3871688 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3871654 GTTTCAAAAT
3871664 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3871689 TGTTTTACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3880249 original size:18 final size:18
Alignment explanation
Indices: 3880226--3880266 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
3880216 TACAAATTAG
* * *
3880226 TATATATGTATATGTAGA
1 TATATATCTATATATACA
3880244 TATATATCTATATATACA
1 TATATATCTATATATACA
3880262 TATAT
1 TATAT
3880267 CTAAAAAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.46
Consensus pattern (18 bp):
TATATATCTATATATACA
Found at i:3888906 original size:20 final size:20
Alignment explanation
Indices: 3888881--3888922 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
3888871 AAACGGCTAT
*
3888881 TCCATTCCCTCCTATTCAAA
1 TCCATTCCCCCCTATTCAAA
*
3888901 TCCATTCCCCCCTATTCCAA
1 TCCATTCCCCCCTATTCAAA
3888921 TC
1 TC
3888923 ACCAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.45, G:0.00, T:0.33
Consensus pattern (20 bp):
TCCATTCCCCCCTATTCAAA
Done.