Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167860.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_13, 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: 22724830
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82000 characters in sequence are not A, C, G, or T
File 8 of 109
Found at i:1341141 original size:31 final size:30
Alignment explanation
Indices: 1341105--1341201 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 30
1341095 ATGTTATGAC
* *
1341105 TTATTTAGGTACAAATTAAAATTTTAAAAGT
1 TTATTTAGGTACAAATTAAAA-ATTAAAAAT
*** * **
1341136 TTATTTCCATATAAATTAAAGGTTAAAAAT
1 TTATTTAGGTACAAATTAAAAATTAAAAAT
*
1341166 TTATTTAGGTGCAAATTAAAAATTAAAAAT
1 TTATTTAGGTACAAATTAAAAATTAAAAAT
1341196 TTATTT
1 TTATTT
1341202 GAATGTAATA
Statistics
Matches: 52, Mismatches: 14, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
30 36 0.69
31 16 0.31
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.42
Consensus pattern (30 bp):
TTATTTAGGTACAAATTAAAAATTAAAAAT
Found at i:1343222 original size:10 final size:10
Alignment explanation
Indices: 1343209--1343238 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1343199 ATCGAATTTT
1343209 TATATTTTAA
1 TATATTTTAA
1343219 TATATTTTAA
1 TATATTTTAA
1343229 T-TATTTTAA
1 TATATTTTAA
1343238 T
1 T
1343239 TAAAAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATTTTAA
Found at i:1343235 original size:9 final size:9
Alignment explanation
Indices: 1343211--1343240 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
1343201 CGAATTTTTA
1343211 TATTTTAAT
1 TATTTTAAT
1343220 ATATTTTAAT
1 -TATTTTAAT
1343230 TATTTTAAT
1 TATTTTAAT
1343239 TA
1 TA
1343241 AAAAATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TATTTTAAT
Found at i:1349063 original size:13 final size:13
Alignment explanation
Indices: 1349045--1349070 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1349035 ATAAAAATCC
1349045 AAAATCCAATTCT
1 AAAATCCAATTCT
1349058 AAAATCCAATTCT
1 AAAATCCAATTCT
1349071 GATATCAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATCCAATTCT
Found at i:1350454 original size:23 final size:23
Alignment explanation
Indices: 1350408--1350453 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 23
1350398 AAGAATGGAG
1350408 AGGAAAGTAAAAGGAAAAGAAAA
1 AGGAAAGTAAAAGGAAAAGAAAA
1350431 AGGAAAG-AAAA-GAAAAGATAAA
1 AGGAAAGTAAAAGGAAAAGA-AAA
1350453 A
1 A
1350454 AATGAGAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.32
22 8 0.36
23 7 0.32
ACGTcount: A:0.72, C:0.00, G:0.24, T:0.04
Consensus pattern (23 bp):
AGGAAAGTAAAAGGAAAAGAAAA
Found at i:1352505 original size:16 final size:16
Alignment explanation
Indices: 1352476--1352509 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1352466 ATTTGAATTG
1352476 TTAAAAAATATATTTT
1 TTAAAAAATATATTTT
1352492 TTAAAGAAAT-TATTTT
1 TTAAA-AAATATATTTT
1352508 TT
1 TT
1352510 TTTATTTTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTAAAAAATATATTTT
Found at i:1356220 original size:15 final size:15
Alignment explanation
Indices: 1356200--1356266 Score: 64
Period size: 15 Copynumber: 4.3 Consensus size: 15
1356190 TAGAGGGTTT
1356200 TAAAATTAAAAAAAA
1 TAAAATTAAAAAAAA
* *
1356215 TAAAATTTAAAAGAA
1 TAAAATTAAAAAAAA
* *
1356230 TAAAGTTTGAAGAAAAA
1 TAAA-ATT-AAAAAAAA
1356247 TAAAA-TAAAATAAAA
1 TAAAATTAAAA-AAAA
1356262 TAAAA
1 TAAAA
1356267 CATTACCAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
14 3 0.07
15 27 0.66
16 2 0.05
17 9 0.22
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (15 bp):
TAAAATTAAAAAAAA
Found at i:1356817 original size:187 final size:187
Alignment explanation
Indices: 1356495--1356874 Score: 733
Period size: 187 Copynumber: 2.0 Consensus size: 187
1356485 TTTGTCACTA
1356495 ATTTTTAAAAGAAAAACAATATTGAAAAAAATGAAAAAAGATAAAATCAAAGATTTATAACATGG
1 ATTTTTAAAAGAAAAACAATATTGAAAAAAATGAAAAAAGATAAAATCAAAGATTTATAACATGG
1356560 ATTAAACTGATCATTCGCATCTTTTAATTTGTGTTTGCATCATTAATTTGTTTAATGTTACATCA
66 ATTAAACTGATCATTCGCATCTTTTAATTTGTGTTTGCATCATTAATTTGTTTAATGTTACATCA
1356625 CTTCTGAGTTATTATTGCCAAAAAACATAAATTAATAAAGAGTGATTTTAAAAGTTT
131 CTTCTGAGTTATTATTGCCAAAAAACATAAATTAATAAAGAGTGATTTTAAAAGTTT
1356682 ATTTTTAAAAGAAAAACAATATTGAAAAAAATGAAAAAAGATAAAATCAAAGATTTATAACATGG
1 ATTTTTAAAAGAAAAACAATATTGAAAAAAATGAAAAAAGATAAAATCAAAGATTTATAACATGG
* * *
1356747 ATTAAACTGGTCATTCGCATCTTTTAATTTGTGTTTGCTTCATTAATTTGTTTAATGTTACATTA
66 ATTAAACTGATCATTCGCATCTTTTAATTTGTGTTTGCATCATTAATTTGTTTAATGTTACATCA
1356812 CTTCTGAGTTATTATTGCCAAAAAACATAAATTAATAAAGAGTGATTTTAAAAGTTT
131 CTTCTGAGTTATTATTGCCAAAAAACATAAATTAATAAAGAGTGATTTTAAAAGTTT
1356869 ATTTTT
1 ATTTTT
1356875 TATTAGAAAT
Statistics
Matches: 190, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
187 190 1.00
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (187 bp):
ATTTTTAAAAGAAAAACAATATTGAAAAAAATGAAAAAAGATAAAATCAAAGATTTATAACATGG
ATTAAACTGATCATTCGCATCTTTTAATTTGTGTTTGCATCATTAATTTGTTTAATGTTACATCA
CTTCTGAGTTATTATTGCCAAAAAACATAAATTAATAAAGAGTGATTTTAAAAGTTT
Found at i:1360404 original size:3 final size:3
Alignment explanation
Indices: 1360390--1360427 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
1360380 CCTTAAACTT
* *
1360390 TTA TTA TGA TTA TTA TTA ATA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1360428 TGATGTAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1361381 original size:21 final size:21
Alignment explanation
Indices: 1361355--1361399 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1361345 TTATATTTAA
*
1361355 AATTATCGAAATTTAA-ATTTT
1 AATTAT-GAAAATTAATATTTT
*
1361376 AATTATTAAAATTAATATTTT
1 AATTATGAAAATTAATATTTT
1361397 AAT
1 AAT
1361400 ATTTTATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
AATTATGAAAATTAATATTTT
Found at i:1363129 original size:14 final size:14
Alignment explanation
Indices: 1363112--1363139 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1363102 TAAAAAAAAA
1363112 TTTAAATCAAATTC
1 TTTAAATCAAATTC
1363126 TTTAAATCAAATTC
1 TTTAAATCAAATTC
1363140 ATAAAATTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (14 bp):
TTTAAATCAAATTC
Found at i:1364410 original size:2 final size:2
Alignment explanation
Indices: 1364403--1364436 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1364393 AATAGAATAC
*
1364403 AT AT AT AT AT AT AT AT AT AT AT TT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1364437 CCTTAGTAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1364877 original size:23 final size:22
Alignment explanation
Indices: 1364837--1364879 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1364827 AACATAAAAA
* *
1364837 ATATATTTTTTATCAAATTTAT
1 ATATAATTTTTATAAAATTTAT
1364859 ATATAATTTTTATTAAAATTT
1 ATATAATTTTTA-TAAAATTT
1364880 TAAATTATTG
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:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
ATATAATTTTTATAAAATTTAT
Found at i:1366138 original size:149 final size:149
Alignment explanation
Indices: 1365868--1366164 Score: 567
Period size: 149 Copynumber: 2.0 Consensus size: 149
1365858 AAACATATGC
1365868 ATGCAATTACAAAGCATATGCTAGCGTTCAAAAATAGAAAAAAAAATTAACTTCAATTTAGGGTT
1 ATGCAATTACAAAGCATATGCTAGCGTTCAAAAATAGAAAAAAAAATTAACTTCAATTTAGGGTT
*
1365933 AAATAATATGGGTTGATTAAAGGGTAAGTAGGTTGAATTACTGCCAATTGATCTACACTTCAACA
66 AAATAATATGGGTTGATTAAAGGGTAAGTAGGTTGAATTACTGCCAATCGATCTACACTTCAACA
*
1365998 GTGCTCCTAGATTTAGCAT
131 GTACTCCTAGATTTAGCAT
1366017 ATGCAATTACAAAGCATATGCTAGCGTTCAAAAATAGAAAAAAAAATTAACTTCAATTTAGGGTT
1 ATGCAATTACAAAGCATATGCTAGCGTTCAAAAATAGAAAAAAAAATTAACTTCAATTTAGGGTT
*
1366082 AAATAATATGGGTTGATTAAAGGGTAAGTAGGTTGAATTACTGCCAATCGATCTACATTTCAACA
66 AAATAATATGGGTTGATTAAAGGGTAAGTAGGTTGAATTACTGCCAATCGATCTACACTTCAACA
1366147 GTACTCCTAGATTTAGCA
131 GTACTCCTAGATTTAGCA
1366165 AAGTCAAACA
Statistics
Matches: 145, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 145 1.00
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.30
Consensus pattern (149 bp):
ATGCAATTACAAAGCATATGCTAGCGTTCAAAAATAGAAAAAAAAATTAACTTCAATTTAGGGTT
AAATAATATGGGTTGATTAAAGGGTAAGTAGGTTGAATTACTGCCAATCGATCTACACTTCAACA
GTACTCCTAGATTTAGCAT
Found at i:1366345 original size:16 final size:15
Alignment explanation
Indices: 1366324--1366356 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 15
1366314 TTATTATTGC
1366324 TATTATTATTTTATAA
1 TATTATTA-TTTATAA
1366340 TATTATTATTTATAA
1 TATTATTATTTATAA
1366355 TA
1 TA
1366357 AATTTTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTATTATTTATAA
Found at i:1366352 original size:20 final size:19
Alignment explanation
Indices: 1366302--1366352 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
1366292 CATGCGTGGG
*
1366302 TTTATT-TTTATTTTATTA
1 TTTATTATTTATTTTATAA
1366320 TTGCTATTA-TTATTTTATAA
1 TT--TATTATTTATTTTATAA
1366340 TATTATTATTTAT
1 T-TTATTATTTAT
1366353 AATAAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
18 2 0.07
19 5 0.19
20 19 0.70
21 1 0.04
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (19 bp):
TTTATTATTTATTTTATAA
Found at i:1366822 original size:11 final size:11
Alignment explanation
Indices: 1366770--1366827 Score: 57
Period size: 11 Copynumber: 5.3 Consensus size: 11
1366760 CATGACAATT
1366770 TAAAATATAATA
1 TAAAA-ATAATA
* *
1366782 TAATAATATTA
1 TAAAAATAATA
*
1366793 CAAAAAGTAATA
1 TAAAAA-TAATA
1366805 T--AAATAATA
1 TAAAAATAATA
1366814 TAAAAATAATA
1 TAAAAATAATA
1366825 TAA
1 TAA
1366828 TTTAAATTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
9 6 0.16
10 3 0.08
11 20 0.54
12 8 0.22
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (11 bp):
TAAAAATAATA
Found at i:1367686 original size:18 final size:17
Alignment explanation
Indices: 1367663--1367709 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 17
1367653 TAGTTTTAAG
1367663 ATAT-TTATTAAAAATT
1 ATATATTATTAAAAATT
1367679 ATATA-T-TTAAAAATT
1 ATATATTATTAAAAATT
1367694 ATATAATTATCTAAAA
1 ATAT-ATTAT-TAAAA
1367710 CTTTCAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 13 0.50
16 6 0.23
17 1 0.04
18 1 0.04
19 5 0.19
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATATTATTAAAAATT
Found at i:1367688 original size:15 final size:15
Alignment explanation
Indices: 1367670--1367698 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1367660 AAGATATTTA
1367670 TTAAAAATTATATAT
1 TTAAAAATTATATAT
1367685 TTAAAAATTATATA
1 TTAAAAATTATATA
1367699 ATTATCTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAAAATTATATAT
Found at i:1368086 original size:14 final size:14
Alignment explanation
Indices: 1368067--1368094 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1368057 GACCAATTAT
1368067 CATATAAATTAGAA
1 CATATAAATTAGAA
1368081 CATATAAATTAGAA
1 CATATAAATTAGAA
1368095 AATAATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (14 bp):
CATATAAATTAGAA
Found at i:1369605 original size:28 final size:30
Alignment explanation
Indices: 1369567--1369638 Score: 94
Period size: 28 Copynumber: 2.5 Consensus size: 30
1369557 TAGAGTTTGA
* * *
1369567 AGATTTTAGGGTTTGGGTTTT-GGGGTTTT
1 AGATTTAAGGGTTTGGATTTTAGGGATTTT
1369596 -GATTTAAGGGTTTGGATTTTAGGGATTTT
1 AGATTTAAGGGTTTGGATTTTAGGGATTTT
*
1369625 AGATTTAAGAGTTT
1 AGATTTAAGGGTTT
1369639 AAAGGTTTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 18 0.49
29 7 0.19
30 12 0.32
ACGTcount: A:0.19, C:0.00, G:0.32, T:0.49
Consensus pattern (30 bp):
AGATTTAAGGGTTTGGATTTTAGGGATTTT
Found at i:1369606 original size:14 final size:14
Alignment explanation
Indices: 1369589--1369638 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
1369579 TTGGGTTTTG
1369589 GGGTTTTGATTTAA
1 GGGTTTTGATTTAA
* *
1369603 GGGTTTGGATTTTA
1 GGGTTTTGATTTAA
1369617 GGGATTTTAGATTTAA
1 GGG-TTTT-GATTTAA
*
1369633 GAGTTT
1 GGGTTT
1369639 AAAGGTTTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
14 15 0.52
15 6 0.21
16 8 0.28
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.48
Consensus pattern (14 bp):
GGGTTTTGATTTAA
Found at i:1369709 original size:15 final size:16
Alignment explanation
Indices: 1369655--1369746 Score: 89
Period size: 16 Copynumber: 5.6 Consensus size: 16
1369645 TTGAAATTTC
1369655 GGATTTTAGGGGATTTT
1 GGATTTTAGGGG-TTTT
*
1369672 AGATTTTAGGGGTTTT
1 GGATTTTAGGGGTTTT
1369688 GGATTTTAGGCGG-TTT
1 GGATTTTAGG-GGTTTT
*
1369704 -GATTTTAAGGGATTTT
1 GGATTTT-AGGGGTTTT
* *
1369720 GAATTTTTAGGGGTTTC
1 GGA-TTTTAGGGGTTTT
*
1369737 GAATTTTAGG
1 GGATTTTAGG
1369747 ATTTGAAAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
15 7 0.11
16 29 0.45
17 24 0.38
18 4 0.06
ACGTcount: A:0.20, C:0.02, G:0.32, T:0.47
Consensus pattern (16 bp):
GGATTTTAGGGGTTTT
Found at i:1371015 original size:26 final size:26
Alignment explanation
Indices: 1370964--1371017 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
1370954 AGCTTCGAAA
**
1370964 AAGGGAGTCCGAGAGAGCTTTTTGGG
1 AAGGGAGTCCGAGAGAGCTTCGTGGG
* *
1370990 AAGGGGGTCTGAGAGAGCTTCGTGGG
1 AAGGGAGTCCGAGAGAGCTTCGTGGG
1371016 AA
1 AA
1371018 AGAAGTAGGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.24, C:0.11, G:0.44, T:0.20
Consensus pattern (26 bp):
AAGGGAGTCCGAGAGAGCTTCGTGGG
Found at i:1371183 original size:14 final size:13
Alignment explanation
Indices: 1371153--1371194 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
1371143 GCCACCCTAC
*
1371153 TTTCTGTTT-TTT
1 TTTCTCTTTCTTT
*
1371165 TTTCTTTTTCTTAT
1 TTTCTCTTTCTT-T
1371179 TTTCTCTTTCTTT
1 TTTCTCTTTCTTT
1371192 TTT
1 TTT
1371195 TAATAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 8 0.31
13 6 0.23
14 12 0.46
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.81
Consensus pattern (13 bp):
TTTCTCTTTCTTT
Found at i:1371195 original size:14 final size:14
Alignment explanation
Indices: 1371161--1371195 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1371151 ACTTTCTGTT
*
1371161 TTTTTTTCTTTTTC
1 TTTTTTTCTCTTTC
*
1371175 TTATTTTCTCTTTC
1 TTTTTTTCTCTTTC
1371189 TTTTTTT
1 TTTTTTT
1371196 AATAATAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTTTCTCTTTC
Found at i:1371552 original size:110 final size:110
Alignment explanation
Indices: 1371398--1371953 Score: 620
Period size: 110 Copynumber: 5.1 Consensus size: 110
1371388 TTTTAAAAAG
* * * * * *
1371398 ACAAAA-CGATTGGGATGACACCATAAGTCGAAAAATAATGAATCGATCGAGATAATATCGCAAA
1 ACAAAATCGACTGGGATAACACCACAAGTTGAAAAATAAAGAATCGATCGAGATAACATCGCAAA
* * * *
1371462 TCAAATTTATGCCCGGAGGTCTTACAAATCATGTCTGAAGGTCTT
66 TCGAATTTATGCCCGGAGGTCTTAGAAATCATGCCCGAAGGTCTT
* * * ** * * **
1371507 ACAGAATCGATTGAGATAACACCGTAAGTTGAAAAATAAAAAATCGATCGAAATAACATCGTGAA
1 ACAAAATCGACTGGGATAACACCACAAGTTGAAAAATAAAGAATCGATCGAGATAACATCGCAAA
* *
1371572 TCGAATTTATGCCCAGAGGTCTTAGAAATCATGCCCGGAGGTCTT
66 TCGAATTTATGCCCGGAGGTCTTAGAAATCATGCCCGAAGGTCTT
* ** * * *
1371617 ACAGAATCGACTAAGATAACATCACAAGTTGAAAGATAAAGAATCGATCGGGATAACA-C-CATA
1 ACAAAATCGACTGGGATAACACCACAAGTTGAAAAATAAAGAATCGATCGAGATAACATCGCA-A
* * *
1371680 ATCGAATTTATGCTCGGAGGTCTTAGAAATCATGCTCGGAGGTCTT
65 ATCGAATTTATGCCCGGAGGTCTTAGAAATCATGCCCGAAGGTCTT
* * * * *
1371726 ACAAAATCAACTGGGATAACACCACAAG-TCAAAAGATAAAAAATCAATCGGGATAACATCGCAA
1 ACAAAATCGACTGGGATAACACCACAAGTTGAAAA-ATAAAGAATCGATCGAGATAACATCGCAA
* ** *
1371790 ATCAAATTTATGCCCGGAGGTCTTAGAAATCATGCCCGAAAATTTT
65 ATCGAATTTATGCCCGGAGGTCTTAGAAATCATGCCCGAAGGTCTT
* *
1371836 ACAAAATCGACTGGGATAACACCACAAG-TCAAAAGATAAAGAATCGATC-AGGATAACATCGCG
1 ACAAAATCGACTGGGATAACACCACAAGTTGAAAA-ATAAAGAATCGATCGA-GATAACATCGCA
* * ** *
1371899 AATCGAATTTATGCCTGGAAGTCTTAGAAATCACACCCGAAGATCTT
64 AATCGAATTTATGCCCGGAGGTCTTAGAAATCATGCCCGAAGGTCTT
1371946 ACAAAATC
1 ACAAAATC
1371954 ATGCCCGAAG
Statistics
Matches: 382, Mismatches: 59, Indels: 11
0.85 0.13 0.02
Matches are distributed among these distances:
108 4 0.01
109 94 0.25
110 282 0.74
111 2 0.01
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (110 bp):
ACAAAATCGACTGGGATAACACCACAAGTTGAAAAATAAAGAATCGATCGAGATAACATCGCAAA
TCGAATTTATGCCCGGAGGTCTTAGAAATCATGCCCGAAGGTCTT
Found at i:1371846 original size:219 final size:221
Alignment explanation
Indices: 1371408--1372276 Score: 777
Period size: 219 Copynumber: 3.9 Consensus size: 221
1371398 ACAAAACGAT
* * * * * *
1371408 TGGGATGACACCATAAGTCGAAAAATAATGAATCGATCGAGATAATATCGCAAATCAAATTTATG
1 TGGGATAACACCACAAGTCGAAAAATAAAGAATCGATCGAGATAACATCGCGAATCGAATTTATG
* * * * * * * * ** * *
1371473 CCCGGAGGTCTTACAAATCATGTCTGAAGGTCTTACAGAATCGATTGAGATAACACCGTAAGTTG
66 CCCGGAAGTCTTAGAAATCATGCCCGAAGGTCTTACAAAATCAACTGGGATAACACCACAAGATC
* * ** * *
1371538 AAAA-ATAAAAAATCGATCGAAATAACATCGTGAATCGAATTTATGCCCAGAGGTCTTAGAAATC
131 AAAAGATAAAAAATCAATCGGAATAACATCGCAAATCAAATTTATGCCCGGAGGTCTTAGAAATC
1371602 ATGCCCGGAGGTCTTACAGAATCGAC
196 ATGCCCGGAGGTCTTACAGAATCGAC
** * * * * *
1371628 TAAGATAACATCACAAGTTGAAAGATAAAGAATCGATCGGGATAACA-C-CATAATCGAATTTAT
1 TGGGATAACACCACAAGTCGAAAAATAAAGAATCGATCGAGATAACATCGC-GAATCGAATTTAT
* * * *
1371691 GCTCGGAGGTCTTAGAAATCATGCTCGGAGGTCTTACAAAATCAACTGGGATAACACCACAAG-T
65 GCCCGGAAGTCTTAGAAATCATGCCCGAAGGTCTTACAAAATCAACTGGGATAACACCACAAGAT
*
1371755 CAAAAGATAAAAAATCAATCGGGATAACATCGCAAATCAAATTTATGCCCGGAGGTCTTAGAAAT
130 CAAAAGATAAAAAATCAATCGGAATAACATCGCAAATCAAATTTATGCCCGGAGGTCTTAGAAAT
* ** * *
1371820 CATGCCCGAAAATTTTACAAAATCGAC
195 CATGCCCGGAGGTCTTACAGAATCGAC
1371847 TGGGATAACACCACAAGTC-AAAAGATAAAGAATCGATC-AGGATAACATCGCGAATCGAATTTA
1 TGGGATAACACCACAAGTCGAAAA-ATAAAGAATCGATCGA-GATAACATCGCGAATCGAATTTA
* ** * * * * * **
1371910 TGCCTGGAAGTCTTAGAAATCACACCCGAAGATCTTACAAAATCATGCCCGAAGGTCTTACAGAA
64 TGCCCGGAAGTCTTAGAAATCATGCCCGAAGGTCTTACAAAATCA--ACTG--GG-ATAACACCA
** * *
1371975 TCGATTAGAATAACACCACAAG-TCAAAAGATAAAAAATCGATCGGGATAACATCGCAAATCGAA
124 -C-A--AG-AT--CA--A-AAGAT--AAA-A-AATCAAT----CGGAATAACATCGCAAATCAAA
* ** * *
1372039 TTTATGCCCGGAGGTCTTAGAAATCATACTTGGAGGTCTTATAGAATTGAC
171 TTTATGCCCGGAGGTCTTAGAAATCATGCCCGGAGGTCTTACAGAATCGAC
* *
1372090 TGGGATAACACCACAAGTC-AAAAATAAAGAATCGATCGAGACAACA-CTGCGAATCGAAATTAT
1 TGGGATAACACCACAAGTCGAAAAATAAAGAATCGATCGAGATAACATC-GCGAATCGAATTTAT
* * * * * *
1372153 GCCCGAAAGTCTTAGAAATCATGCCCGAAGGTCTTATAGAATCGATTGGAATAACACCACAAG-T
65 GCCCGGAAGTCTTAGAAATCATGCCCGAAGGTCTTACAAAATCAACTGGGATAACACCACAAGAT
* * * *
1372217 CAAAAGATAAAAAATCGATCGGAATAACATCGCGAATCAAATTTATACCCGGAAGTCTTA
130 CAAAAGATAAAAAATCAATCGGAATAACATCGCAAATCAAATTTATGCCCGGAGGTCTTA
1372277 CATATCTCAA
Statistics
Matches: 519, Mismatches: 97, Indels: 67
0.76 0.14 0.10
Matches are distributed among these distances:
218 9 0.02
219 209 0.40
220 86 0.17
221 1 0.00
222 2 0.00
223 4 0.01
224 3 0.01
225 8 0.02
226 4 0.01
227 3 0.01
229 4 0.01
231 2 0.00
233 4 0.01
235 3 0.01
236 4 0.01
237 8 0.02
238 2 0.00
239 5 0.01
240 1 0.00
241 1 0.00
242 70 0.13
243 86 0.17
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (221 bp):
TGGGATAACACCACAAGTCGAAAAATAAAGAATCGATCGAGATAACATCGCGAATCGAATTTATG
CCCGGAAGTCTTAGAAATCATGCCCGAAGGTCTTACAAAATCAACTGGGATAACACCACAAGATC
AAAAGATAAAAAATCAATCGGAATAACATCGCAAATCAAATTTATGCCCGGAGGTCTTAGAAATC
ATGCCCGGAGGTCTTACAGAATCGAC
Found at i:1371945 original size:22 final size:22
Alignment explanation
Indices: 1371916--1371976 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 22
1371906 TTTATGCCTG
*
1371916 GAAGTCTTA-GAAATCACACCC
1 GAAGTCTTACAAAATCACACCC
**
1371937 GAAGATCTTACAAAATCATGCCC
1 GAAG-TCTTACAAAATCACACCC
*
1371960 GAAGGTCTTACAGAATC
1 GAA-GTCTTACAAAATC
1371977 GATTAGAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 4 0.12
22 5 0.15
23 23 0.70
24 1 0.03
ACGTcount: A:0.38, C:0.25, G:0.16, T:0.21
Consensus pattern (22 bp):
GAAGTCTTACAAAATCACACCC
Found at i:1371953 original size:23 final size:23
Alignment explanation
Indices: 1371926--1371976 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1371916 GAAGTCTTAG
1371926 AAATCACACCCGAAGATCTTACA
1 AAATCACACCCGAAGATCTTACA
** *
1371949 AAATCATGCCCGAAGGTCTTACA
1 AAATCACACCCGAAGATCTTACA
*
1371972 GAATC
1 AAATC
1371977 GATTAGAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.39, C:0.27, G:0.14, T:0.20
Consensus pattern (23 bp):
AAATCACACCCGAAGATCTTACA
Found at i:1371992 original size:133 final size:133
Alignment explanation
Indices: 1371816--1372064 Score: 390
Period size: 133 Copynumber: 1.9 Consensus size: 133
1371806 GAGGTCTTAG
* * * *
1371816 AAATCATGCCCGAAAATTTTACAAAATCGACTGGGATAACACCACAAGTCAAAAGATAAAGAATC
1 AAATCATGCCCGAAAATCTTACAAAATCGACTAGAATAACACCACAAGTCAAAAGATAAAAAATC
* *
1371881 GATCAGGATAACATCGCGAATCGAATTTATGCCTGGAAGTCTTAGAAATCACACCCGAAGATCTT
66 GATCAGGATAACATCGCAAATCGAATTTATGCCCGGAAGTCTTAGAAATCACACCCGAAGATCTT
1371946 ACA
131 ACA
** * *
1371949 AAATCATGCCCGAAGGTCTTACAGAATCGATTAGAATAACACCACAAGTCAAAAGATAAAAAATC
1 AAATCATGCCCGAAAATCTTACAAAATCGACTAGAATAACACCACAAGTCAAAAGATAAAAAATC
* *
1372014 GATCGGGATAACATCGCAAATCGAATTTATGCCCGGAGGTCTTAGAAATCA
66 GATCAGGATAACATCGCAAATCGAATTTATGCCCGGAAGTCTTAGAAATCA
1372065 TACTTGGAGG
Statistics
Matches: 104, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
133 104 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.21
Consensus pattern (133 bp):
AAATCATGCCCGAAAATCTTACAAAATCGACTAGAATAACACCACAAGTCAAAAGATAAAAAATC
GATCAGGATAACATCGCAAATCGAATTTATGCCCGGAAGTCTTAGAAATCACACCCGAAGATCTT
ACA
Found at i:1372079 original size:133 final size:132
Alignment explanation
Indices: 1371802--1372079 Score: 385
Period size: 133 Copynumber: 2.1 Consensus size: 132
1371792 CAAATTTATG
* * * *
1371802 CCCGGAGGTCTTAGAAATCATGCCCGAAAATTTTACAAAATCGACTGGGATAACACCACAAGTCA
1 CCCGGAGGTCTTAAAAATCATGCCCGAAAATCTTACAAAATCGACTAGAATAACACCACAAGTCA
* * *
1371867 AAAGATAAAGAATCGATCAGGATAACATCGCGAATCGAATTTATGCCTGGAAGTCTTAGAAATCA
66 AAAGATAAAAAATCGATCAGGATAACATCGCAAATCGAATTTATGCCCGGAAGTCTTAGAAATCA
1371932 CA
131 CA
* * ** * *
1371934 CCCGAAGATCTTACAAAATCATGCCCGAAGGTCTTACAGAATCGATTAGAATAACACCACAAGTC
1 CCCGGAGGTCTTA-AAAATCATGCCCGAAAATCTTACAAAATCGACTAGAATAACACCACAAGTC
* *
1371999 AAAAGATAAAAAATCGATCGGGATAACATCGCAAATCGAATTTATGCCCGGAGGTCTTAGAAATC
65 AAAAGATAAAAAATCGATCAGGATAACATCGCAAATCGAATTTATGCCCGGAAGTCTTAGAAATC
*
1372064 ATA
130 ACA
**
1372067 CTTGGAGGTCTTA
1 CCCGGAGGTCTTA
1372080 TAGAATTGAC
Statistics
Matches: 125, Mismatches: 20, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
132 11 0.09
133 114 0.91
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.22
Consensus pattern (132 bp):
CCCGGAGGTCTTAAAAATCATGCCCGAAAATCTTACAAAATCGACTAGAATAACACCACAAGTCA
AAAGATAAAAAATCGATCAGGATAACATCGCAAATCGAATTTATGCCCGGAAGTCTTAGAAATCA
CA
Found at i:1372101 original size:110 final size:110
Alignment explanation
Indices: 1371949--1372276 Score: 444
Period size: 109 Copynumber: 3.0 Consensus size: 110
1371939 AGATCTTACA
* * * *
1371949 AAATCATGCCCGAAGGTCTTACAGAATCGATTAGAATAACACCACAAGTCAAAAGATAAAAAATC
1 AAATCATACCCGAAGGTCTTATAGAATCGACTGGAATAACACCACAAGTCAAAAGATAAAAAATC
* *
1372014 GATCGGGATAACATCGCAAATCGAATTTATGCCCGGAGGTCTTAG
66 GATCGGGATAACATCGCGAATCGAATTTATGCCCGGAAGTCTTAG
** * * * *
1372059 AAATCATACTTGGAGGTCTTATAGAATTGACTGGGATAACACCACAAGTCAAAA-ATAAAGAATC
1 AAATCATACCCGAAGGTCTTATAGAATCGACTGGAATAACACCACAAGTCAAAAGATAAAAAATC
* * * *
1372123 GATCGAGACAACA-CTGCGAATCGAAATTATGCCCGAAAGTCTTAG
66 GATCGGGATAACATC-GCGAATCGAATTTATGCCCGGAAGTCTTAG
* *
1372168 AAATCATGCCCGAAGGTCTTATAGAATCGATTGGAATAACACCACAAGTCAAAAGATAAAAAATC
1 AAATCATACCCGAAGGTCTTATAGAATCGACTGGAATAACACCACAAGTCAAAAGATAAAAAATC
* * *
1372233 GATCGGAATAACATCGCGAATCAAATTTATACCCGGAAGTCTTA
66 GATCGGGATAACATCGCGAATCGAATTTATGCCCGGAAGTCTTA
1372277 CATATCTCAA
Statistics
Matches: 184, Mismatches: 31, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
108 1 0.01
109 93 0.51
110 89 0.48
111 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (110 bp):
AAATCATACCCGAAGGTCTTATAGAATCGACTGGAATAACACCACAAGTCAAAAGATAAAAAATC
GATCGGGATAACATCGCGAATCGAATTTATGCCCGGAAGTCTTAG
Found at i:1372176 original size:22 final size:22
Alignment explanation
Indices: 1372145--1372188 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1372135 ACTGCGAATC
*
1372145 GAAATTATGCCCGAAAGTCTTA
1 GAAATCATGCCCGAAAGTCTTA
*
1372167 GAAATCATGCCCGAAGGTCTTA
1 GAAATCATGCCCGAAAGTCTTA
1372189 TAGAATCGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.25
Consensus pattern (22 bp):
GAAATCATGCCCGAAAGTCTTA
Found at i:1372246 original size:352 final size:352
Alignment explanation
Indices: 1371597--1372276 Score: 985
Period size: 352 Copynumber: 1.9 Consensus size: 352
1371587 GAGGTCTTAG
* * ** *
1371597 AAATCATGCCCGGAGGTCTTACAGAATCGACTAAGATAACATCACAAGTTGAAAGATAAAGAATC
1 AAATCATGCCCGAAGGTCTTACAGAATCGACTAAGATAACACCACAAGTCAAAAGATAAAAAATC
* *
1371662 GATCGGGATAACACCATAATCGAATTTATGCTCGGAGGTCTTAGAAATCATGCTCGGAGGTCTTA
66 GATCGGGATAACACCATAATCGAATTTATGCCCGGAGGTCTTAGAAATCATACTCGGAGGTCTTA
* *
1371727 CAAAATCAACTGGGATAACACCACAAGTCAAAAGATAAAAAATCAATCGGGATAACATCGCAAAT
131 CAAAATCAACTGGGATAACACCACAAGTCAAAAGATAAAAAATCAATCGAGACAACATCGCAAAT
* * * *
1371792 CAAATTTATGCCCGGAGGTCTTAGAAATCATGCCCGAAAATTTTACAAAATCGACTGGGATAACA
196 CAAATTTATGCCCGAAAGTCTTAGAAATCATGCCCGAAAATCTTACAAAATCGACTGGAATAACA
* * * *
1371857 CCACAAGTCAAAAGATAAAGAATCGATCAGGATAACATCGCGAATCGAATTTATGCCTGGAAGTC
261 CCACAAGTCAAAAGATAAAAAATCGATCAGGATAACATCGCGAATCAAATTTATACCCGGAAGTC
1371922 TTAGAAATCACACCCGAAGATCTTACA
326 TTAGAAATCACACCCGAAGATCTTACA
*
1371949 AAATCATGCCCGAAGGTCTTACAGAATCGA-TTAGAATAACACCACAAGTCAAAAGATAAAAAAT
1 AAATCATGCCCGAAGGTCTTACAGAATCGACTAAG-ATAACACCACAAGTCAAAAGATAAAAAAT
*
1372013 CGATCGGGATAACATCGCA-AATCGAATTTATGCCCGGAGGTCTTAGAAATCATACTTGGAGGTC
65 CGATCGGGATAACA-C-CATAATCGAATTTATGCCCGGAGGTCTTAGAAATCATACTCGGAGGTC
* * ** * *
1372077 TTATAGAATTGACTGGGATAACACCACAAGTCAAAA-ATAAAGAATCGATCGAGACAACA-CTGC
128 TTACAAAATCAACTGGGATAACACCACAAGTCAAAAGATAAAAAATCAATCGAGACAACATC-GC
* ** * * *
1372140 GAATCGAAA-TTATGCCCGAAAGTCTTAGAAATCATGCCCGAAGGTCTTATAGAATCGATTGGAA
192 AAATC-AAATTTATGCCCGAAAGTCTTAGAAATCATGCCCGAAAATCTTACAAAATCGACTGGAA
1372204 TAACACCACAAGTCAAAAGATAAAAAATCGATC-GGAATAACATCGCGAATCAAATTTATACCCG
256 TAACACCACAAGTCAAAAGATAAAAAATCGATCAGG-ATAACATCGCGAATCAAATTTATACCCG
1372268 GAAGTCTTA
320 GAAGTCTTA
1372277 CATATCTCAA
Statistics
Matches: 291, Mismatches: 31, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
351 6 0.02
352 205 0.70
353 78 0.27
354 2 0.01
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (352 bp):
AAATCATGCCCGAAGGTCTTACAGAATCGACTAAGATAACACCACAAGTCAAAAGATAAAAAATC
GATCGGGATAACACCATAATCGAATTTATGCCCGGAGGTCTTAGAAATCATACTCGGAGGTCTTA
CAAAATCAACTGGGATAACACCACAAGTCAAAAGATAAAAAATCAATCGAGACAACATCGCAAAT
CAAATTTATGCCCGAAAGTCTTAGAAATCATGCCCGAAAATCTTACAAAATCGACTGGAATAACA
CCACAAGTCAAAAGATAAAAAATCGATCAGGATAACATCGCGAATCAAATTTATACCCGGAAGTC
TTAGAAATCACACCCGAAGATCTTACA
Found at i:1373205 original size:99 final size:99
Alignment explanation
Indices: 1373010--1373552 Score: 526
Period size: 99 Copynumber: 5.5 Consensus size: 99
1373000 GAAGGTAAGC
* * * * *
1373010 TAAATTGGGCTT-AAGACCTCATTTAAGGCTAGATAAACTAGGCTTAAA-TATCATTGATGGCCA
1 TAAACTGGGCTTAAAG-CTTCATTTAAGGCCAGATAAACTGGGCTTAAAGCATCATTGATGGCCA
* * *
1373073 GATAAACTGGGCTTAAATCTTTATTTAA-AGCCAGA
65 GATAAACTGGGCTTAAAACTTCA-TTAATGGCCAGA
* * * * * *
1373108 TAAACTAGGCTTAAAGCCTCATTTAAGGCCAGATAAACTGGGTTTAAAGCCTTATTGATGGCCAA
1 TAAACTGGGCTTAAAGCTTCATTTAAGGCCAGATAAACTGGGCTTAAAGCATCATTGATGGCCAG
* * *
1373173 ATAAACTAGACTTAAAACTTTATTAATGGCCAGA
66 ATAAACTGGGCTTAAAACTTCATTAATGGCCAGA
* * * *
1373207 TAAACTGGGCTTAAAACTTCATTTGAGGCCAGATAAACTGGGTTTAAAGCGTCATTGATGGCCAG
1 TAAACTGGGCTTAAAGCTTCATTTAAGGCCAGATAAACTGGGCTTAAAGCATCATTGATGGCCAG
* * * **
1373272 ATAAACTGAGCTTAAAGCTTAATTAATGGTTAGA
66 ATAAACTGGGCTTAAAACTTCATTAATGGCCAGA
* * *
1373306 TAAACTGGGCTTAAAACTTCATTTGAA-GCCAAATAAACTGGGTTTAAAGCATCATTGATGGCCA
1 TAAACTGGGCTTAAAGCTTCATTT-AAGGCCAGATAAACTGGGCTTAAAGCATCATTGATGGCCA
**
1373370 GATAAACTGGGCTT-AAA-TGTCATTGTTGGCCAGA
65 GATAAACTGGGCTTAAAACT-TCATTAATGGCCAGA
* * * * ** * * * *
1373404 TAAATTGGGCTTAAAAGTTTCATTGAGGGTTAGATAAACTGGGCTTAAATCTTCATTTGA-AGCT
1 TAAACTGGGCTT-AAAGCTTCATTTAAGGCCAGATAAACTGGGCTTAAAGCATCA-TTGATGGCC
* * * * * *
1373468 AGATAAATTGGGTTTAAAGCCTCATTGATGGCCATA
64 AGATAAACTGGGCTTAAAACTTCATTAATGGCCAGA
* *
1373504 TAAACTAGGCTTAAAGCTTCA-TTAATGGTCAGATAAACTGGGCTTAAAG
1 TAAACTGGGCTTAAAGCTTCATTTAA-GGCCAGATAAACTGGGCTTAAAG
1373553 TTTTTTCTTT
Statistics
Matches: 371, Mismatches: 63, Indels: 21
0.82 0.14 0.05
Matches are distributed among these distances:
97 1 0.00
98 69 0.19
99 271 0.73
100 30 0.08
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (99 bp):
TAAACTGGGCTTAAAGCTTCATTTAAGGCCAGATAAACTGGGCTTAAAGCATCATTGATGGCCAG
ATAAACTGGGCTTAAAACTTCATTAATGGCCAGA
Found at i:1373552 original size:33 final size:33
Alignment explanation
Indices: 1373010--1373552 Score: 439
Period size: 33 Copynumber: 16.5 Consensus size: 33
1373000 GAAGGTAAGC
* * *
1373010 TAAATTGGGCTT-AAGACCTCATTTAA-GGCTAGA
1 TAAACTGGGCTTAAAG-CTTCA-TTAATGGCCAGA
* *
1373043 TAAACTAGGCTTAAA--TATCATTGATGGCCAGA
1 TAAACTGGGCTTAAAGCT-TCATTAATGGCCAGA
* * *
1373075 TAAACTGGGCTTAAATCTTTATTTAA-AGCCAGA
1 TAAACTGGGCTTAAAGCTTCA-TTAATGGCCAGA
* *
1373108 TAAACTAGGCTTAAAGCCTCATTTAA-GGCCAGA
1 TAAACTGGGCTTAAAGCTTCA-TTAATGGCCAGA
* * *
1373141 TAAACTGGGTTTAAAGCCTT-ATTGATGGCCAAA
1 TAAACTGGGCTTAAAG-CTTCATTAATGGCCAGA
* * * *
1373174 TAAACTAGACTTAAAACTTTATTAATGGCCAGA
1 TAAACTGGGCTTAAAGCTTCATTAATGGCCAGA
* *
1373207 TAAACTGGGCTTAAAACTTCATTTGA-GGCCAGA
1 TAAACTGGGCTTAAAGCTTCA-TTAATGGCCAGA
* * *
1373240 TAAACTGGGTTTAAAGCGTCATTGATGGCCAGA
1 TAAACTGGGCTTAAAGCTTCATTAATGGCCAGA
* * **
1373273 TAAACTGAGCTTAAAGCTTAATTAATGGTTAGA
1 TAAACTGGGCTTAAAGCTTCATTAATGGCCAGA
* *
1373306 TAAACTGGGCTTAAAACTTCATT--TGAAGCCAAA
1 TAAACTGGGCTTAAAGCTTCATTAATG--GCCAGA
* * *
1373339 TAAACTGGGTTTAAAGCATCATTGATGGCCAGA
1 TAAACTGGGCTTAAAGCTTCATTAATGGCCAGA
**
1373372 TAAACTGGGCTTAAA--TGTCATTGTTGGCCAGA
1 TAAACTGGGCTTAAAGCT-TCATTAATGGCCAGA
* * * * **
1373404 TAAATTGGGCTTAAAAGTTTCATTGAGGGTTAGA
1 TAAACTGGGCTT-AAAGCTTCATTAATGGCCAGA
* *
1373438 TAAACTGGGCTTAAATCTTCATT--TGAAGCTAGA
1 TAAACTGGGCTTAAAGCTTCATTAATG--GCCAGA
* * * * *
1373471 TAAATTGGGTTTAAAGCCTCATTGATGGCCATA
1 TAAACTGGGCTTAAAGCTTCATTAATGGCCAGA
* *
1373504 TAAACTAGGCTTAAAGCTTCATTAATGGTCAGA
1 TAAACTGGGCTTAAAGCTTCATTAATGGCCAGA
1373537 TAAACTGGGCTTAAAG
1 TAAACTGGGCTTAAAG
1373553 TTTTTTCTTT
Statistics
Matches: 411, Mismatches: 76, Indels: 46
0.77 0.14 0.09
Matches are distributed among these distances:
31 6 0.01
32 58 0.14
33 309 0.75
34 33 0.08
35 5 0.01
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (33 bp):
TAAACTGGGCTTAAAGCTTCATTAATGGCCAGA
Found at i:1374866 original size:12 final size:10
Alignment explanation
Indices: 1374843--1374881 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1374833 CCATAACCAA
1374843 TTTTTTTTTC
1 TTTTTTTTTC
*
1374853 TTTTTTTCTC
1 TTTTTTTTTC
* *
1374863 TCTTTTTTTG
1 TTTTTTTTTC
1374873 TTTTTTTTT
1 TTTTTTTTT
1374882 ATACCCCCAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.87
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:1377830 original size:59 final size:58
Alignment explanation
Indices: 1377654--1378048 Score: 399
Period size: 59 Copynumber: 6.7 Consensus size: 58
1377644 TTGTGCAGAG
* * * * *
1377654 AAAATTGATACTTTCAACTTTTTCC-C-AAAA-TATCTTTTGAAACTTTAATTTTAAGG
1 AAAATTGATACTTTCAA-TTTTTCCTCAAAAATTTTTTTTTGAAAATTTATTTTTAAGA
* * **
1377710 AAAATTGATACTTTCAACTTTTCCTAAAAAAAAAACCTTTTTTT-AAAATTTATTTTTAAGA
1 AAAATTGATACTTTCAATTTTTCCT----CAAAAATTTTTTTTTGAAAATTTATTTTTAAGA
1377771 AAAATTGATACTTTCAATTTTTCCTCAAAAACTTTTTTTTTGAAAATTTATTTTTAAGA
1 AAAATTGATACTTTCAATTTTTCCTCAAAAA-TTTTTTTTTGAAAATTTATTTTTAAGA
* * * ** *
1377830 AAAATTGATACTTTCAACTTTTTCC-CAAAAATATTTTTTGGAAACTTTGATTTTCGAGG
1 AAAATTGATACTTTCAA-TTTTTCCTCAAAAATTTTTTTTTGAAAATTT-ATTTTTAAGA
* * *
1377889 AAAACTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTTTTTAAAAATTTATTTTTAAGA
1 AAAATTGATACTTTCAATTTTTCCTCAAAAA---TTTTTTTTTGAAAATTTATTTTTAAGA
* * ** *
1377950 AAAATTGATACTTTCAACTTTTTCCT--AAAATATTTTTTTGAAACTTTGATTTTCGAGG
1 AAAATTGATACTTTCAA-TTTTTCCTCAAAAATTTTTTTTTGAAAATTT-ATTTTTAAGA
*
1378008 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTT
1 AAAATTGATACTTTCAATTTTTCCTCAAAAAT-TTTTTTTT
1378049 AAATCTTTTT
Statistics
Matches: 282, Mismatches: 37, Indels: 36
0.79 0.10 0.10
Matches are distributed among these distances:
55 6 0.02
56 17 0.06
57 26 0.09
58 51 0.18
59 74 0.26
60 18 0.06
61 65 0.23
62 25 0.09
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.45
Consensus pattern (58 bp):
AAAATTGATACTTTCAATTTTTCCTCAAAAATTTTTTTTTGAAAATTTATTTTTAAGA
Found at i:1378060 original size:119 final size:117
Alignment explanation
Indices: 1377653--1378051 Score: 501
Period size: 120 Copynumber: 3.4 Consensus size: 117
1377643 CTTGTGCAGA
* * * * *
1377653 GAAAATTGATACTTTCAACTTTTTCC-C-AAAA-TA-TCTTTTGAAACTTTAATTTTAAGGAAAA
1 GAAAATTGATACTTTCAAC-TTTTCCTCAAAAACTATTTTTTTTAAAATTTATTTTTAAGAAAAA
* * **
1377714 TTGATACTTTCAAC-TTTTCCTAAAAAAAAAACCTTTTTTT-AAAATTT-ATTTTTAAG
65 TTGATACTTTCAACTTTTTCCT----AAAATA--TTTTTTTGAAACTTTGATTTTCGAG
* *
1377770 AAAAATTGATACTTTCAATTTTTCCTCAAAAACT-TTTTTTTTGAAAATTTATTTTTAAGAAAAA
1 GAAAATTGATACTTTCAACTTTTCCTCAAAAACTATTTTTTTT-AAAATTTATTTTTAAGAAAAA
* *
1377834 TTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGGAAACTTTGATTTTCGAG
65 TTGATACTTTCAACTTTTT-CCTAAAATATTTTTTTGAAACTTTGATTTTCGAG
* *
1377888 GAAAACTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTTTTTAAAAATTTATTTTTAAGAAAA
1 GAAAATTGATACTTTCAACTTTTCCTCAAAAA-CTATTTTTTTT-AAAATTTATTTTTAAGAAAA
1377953 ATTGATACTTTCAACTTTTTCCTAAAATATTTTTTTGAAACTTTGATTTTCGAG
64 ATTGATACTTTCAACTTTTTCCTAAAATATTTTTTTGAAACTTTGATTTTCGAG
1378007 GAAAATTGATACTTTCAACTTTTCCTCAAAAA-TATTTTTTTTAAA
1 GAAAATTGATACTTTCAACTTTTCCTCAAAAACTATTTTTTTTAAA
1378052 TCTTTTTATC
Statistics
Matches: 250, Mismatches: 21, Indels: 23
0.85 0.07 0.08
Matches are distributed among these distances:
116 15 0.06
117 33 0.13
118 45 0.18
119 71 0.28
120 80 0.32
121 4 0.02
122 2 0.01
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.45
Consensus pattern (117 bp):
GAAAATTGATACTTTCAACTTTTCCTCAAAAACTATTTTTTTTAAAATTTATTTTTAAGAAAAAT
TGATACTTTCAACTTTTTCCTAAAATATTTTTTTGAAACTTTGATTTTCGAG
Found at i:1379894 original size:28 final size:28
Alignment explanation
Indices: 1379862--1379925 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 28
1379852 CTGGGTAAAA
* * * *
1379862 AGAGAAGTGGTTGTCGGTGTCTTGGGGC
1 AGAGAAGCGGGTGTCGGCGCCTTGGGGC
1379890 AGAGAAGCGGGTGTCGGCGCCTTGGGGC
1 AGAGAAGCGGGTGTCGGCGCCTTGGGGC
1379918 AGAGAAGC
1 AGAGAAGC
1379926 TCGATGAAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.19, C:0.16, G:0.47, T:0.19
Consensus pattern (28 bp):
AGAGAAGCGGGTGTCGGCGCCTTGGGGC
Found at i:1380175 original size:20 final size:17
Alignment explanation
Indices: 1380136--1380173 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 17
1380126 TTTATCAGAT
1380136 AATCAAAAAAAAAAATA
1 AATCAAAAAAAAAAATA
1380153 AATCATAAAAATAAAAATA
1 AATCA-AAAAA-AAAAATA
1380172 AA
1 AA
1380174 ATTGATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.26
18 5 0.26
19 9 0.47
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.16
Consensus pattern (17 bp):
AATCAAAAAAAAAAATA
Found at i:1384240 original size:16 final size:16
Alignment explanation
Indices: 1384154--1384381 Score: 92
Period size: 16 Copynumber: 14.8 Consensus size: 16
1384144 ATATGGAAGG
1384154 TTTA-GGATTTT-GAT
1 TTTAGGGATTTTGGAT
* *
1384168 TTTAGAG-TTTGGAGAT
1 TTTAGGGATTTTG-GAT
*
1384184 TTTAGGG-TTTCGG-T
1 TTTAGGGATTTTGGAT
1384198 TTT-GAGG-TTTT-GAT
1 TTTAG-GGATTTTGGAT
*
1384212 TTAAGGG--TTTGGAT
1 TTTAGGGATTTTGGAT
*
1384226 TTTAGGAATTTTGGAT
1 TTTAGGGATTTTGGAT
* * *
1384242 TTAAGAG-TTTAAAGG--
1 TTTAGGGATTT--TGGAT
* *
1384257 TTT-GGAATTTCGGAT
1 TTTAGGGATTTTGGAT
* *
1384272 TTTGGGGGGTTTTGGAT
1 TTT-AGGGATTTTGGAT
*
1384289 TTTAGGGATTTCGGAT
1 TTTAGGGATTTTGGAT
*
1384305 TTTAGGCG-GTTTGGAT
1 TTTAGG-GATTTTGGAT
* *
1384321 TTAAGGGACTTTGGAT
1 TTTAGGGATTTTGGAT
* *
1384337 TTAAGGGATTTTAGATT
1 TTTAGGGATTTTGGA-T
* * *
1384354 TTTAGGGGTTTCGAAT
1 TTTAGGGATTTTGGAT
1384370 TTTA-GGATTTTG
1 TTTAGGGATTTTG
1384382 AAAATTAAAA
Statistics
Matches: 160, Mismatches: 35, Indels: 37
0.69 0.15 0.16
Matches are distributed among these distances:
13 7 0.04
14 30 0.19
15 21 0.13
16 76 0.47
17 26 0.16
ACGTcount: A:0.20, C:0.03, G:0.31, T:0.46
Consensus pattern (16 bp):
TTTAGGGATTTTGGAT
Found at i:1384328 original size:32 final size:33
Alignment explanation
Indices: 1384263--1384375 Score: 106
Period size: 33 Copynumber: 3.5 Consensus size: 33
1384253 AAGGTTTGGA
* * *
1384263 ATTTCGGATTTTGGGGGGTTTTGGATTTTAGGG
1 ATTTCGGATTTTAGGCGGTTTTGGATTTAAGGG
1384296 ATTTCGGATTTTAGGCGG-TTTGGATTTAAGGG
1 ATTTCGGATTTTAGGCGGTTTTGGATTTAAGGG
* * * *
1384328 ACTTT-GGATTTAAGG-GATTTTAGATTTTTAGGG
1 A-TTTCGGATTTTAGGCGGTTTTGGA-TTTAAGGG
* *
1384361 GTTTCGAATTTTAGG
1 ATTTCGGATTTTAGG
1384376 ATTTTGAAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 8
0.79 0.12 0.10
Matches are distributed among these distances:
31 1 0.02
32 31 0.47
33 34 0.52
ACGTcount: A:0.19, C:0.04, G:0.33, T:0.44
Consensus pattern (33 bp):
ATTTCGGATTTTAGGCGGTTTTGGATTTAAGGG
Found at i:1385630 original size:26 final size:26
Alignment explanation
Indices: 1385594--1385659 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
1385584 AGGGCTGTGT
*
1385594 GTCCGAAAGAGCTTTCGAAAAGGGGA
1 GTCCGAGAGAGCTTTCGAAAAGGGGA
* **
1385620 GTCCGAGAGAGCTTTTTGGGAAGGGGA
1 GTCCGAGAGAGC-TTTCGAAAAGGGGA
1385647 -TCCGAGAGAGCTT
1 GTCCGAGAGAGCTT
1385660 CGTGAGGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
25 2 0.06
26 22 0.63
27 11 0.31
ACGTcount: A:0.27, C:0.15, G:0.38, T:0.20
Consensus pattern (26 bp):
GTCCGAGAGAGCTTTCGAAAAGGGGA
Found at i:1385668 original size:27 final size:27
Alignment explanation
Indices: 1385613--1385668 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
1385603 AGCTTTCGAA
**
1385613 AAGGGGAGTCCGAGAGAGCTTTTTGGG
1 AAGGGGAGTCCGAGAGAGCTTCGTGGG
1385640 AAGGGGA-TCCGAGAGAGCTTCGTGAGG
1 AAGGGGAGTCCGAGAGAGCTTCGTG-GG
1385667 AA
1 AA
1385669 AAAAGTAGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.27, C:0.12, G:0.43, T:0.18
Consensus pattern (27 bp):
AAGGGGAGTCCGAGAGAGCTTCGTGGG
Found at i:1386841 original size:19 final size:18
Alignment explanation
Indices: 1386808--1386846 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1386798 TATTATAGTA
* *
1386808 TAATATATTATATCATAT
1 TAATATATTACATCACAT
1386826 TAATATTATTACATCACAT
1 TAATA-TATTACATCACAT
1386845 TA
1 TA
1386847 CGATTACTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATATATTACATCACAT
Found at i:1388765 original size:14 final size:15
Alignment explanation
Indices: 1388748--1388805 Score: 68
Period size: 14 Copynumber: 3.9 Consensus size: 15
1388738 TTGCATGCAT
1388748 TTATTTTAATT-TTA
1 TTATTTTAATTATTA
1388762 TTATTTTAATTATTA
1 TTATTTTAATTATTA
*
1388777 TT-TTTTAAATATT-
1 TTATTTTAATTATTA
1388790 TTATTTATAATATATT
1 TTATTT-TAAT-TATT
1388806 TCAATTTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
13 2 0.05
14 24 0.63
15 8 0.21
16 4 0.11
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATTTTAATTATTA
Found at i:1389565 original size:21 final size:21
Alignment explanation
Indices: 1389536--1389576 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1389526 TTTATGTTCA
*
1389536 AATATAATTATTTA-AAATATG
1 AATAAAATTA-TTACAAATATG
1389557 AATAAAATTATTACAAATAT
1 AATAAAATTATTACAAATAT
1389577 TAATTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
AATAAAATTATTACAAATATG
Found at i:1392550 original size:14 final size:14
Alignment explanation
Indices: 1392531--1392567 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
1392521 AAATAGATAT
1392531 AATACAATTTATTA
1 AATACAATTTATTA
1392545 AATACAATTTATTA
1 AATACAATTTATTA
1392559 AATACAATT
1 AATACAATT
1392568 ATGTAGCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (14 bp):
AATACAATTTATTA
Found at i:1393352 original size:26 final size:23
Alignment explanation
Indices: 1393317--1393382 Score: 80
Period size: 26 Copynumber: 2.7 Consensus size: 23
1393307 AATATAAAAT
1393317 ATAAAAAATATATATTTAA-AATTTTA
1 ATAAAAAATATATATTTAATAA----A
*
1393343 ATAAAAAATATAAATTTAATAAA
1 ATAAAAAATATATATTTAATAAA
1393366 ATAAAAAATATATATTT
1 ATAAAAAATATATATTT
1393383 CGTGTAAACG
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
23 17 0.46
26 18 0.49
27 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
ATAAAAAATATATATTTAATAAA
Found at i:1394139 original size:31 final size:30
Alignment explanation
Indices: 1394103--1394196 Score: 74
Period size: 31 Copynumber: 3.2 Consensus size: 30
1394093 TTTTTTTGGA
1394103 AACTTTAATTTCAAGGAAAATTGATACTTTC
1 AACTTTAATTTCAAGGAAAATTGAT-CTTTC
* * *
1394134 AACTTT--TCCTCAA--AAAATT--TTTTTGA
1 AACTTTAAT-TTCAAGGAAAATTGATCTTT-C
*
1394160 AACTTTAATTTCGAGGAAAATTGATGCTTTC
1 AACTTTAATTTCAAGGAAAATTGAT-CTTTC
1394191 AACTTT
1 AACTTT
1394197 TCCTCAAAAC
Statistics
Matches: 47, Mismatches: 7, Indels: 18
0.65 0.10 0.25
Matches are distributed among these distances:
25 3 0.06
26 7 0.15
27 3 0.06
28 7 0.15
29 7 0.15
30 4 0.09
31 13 0.28
32 3 0.06
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (30 bp):
AACTTTAATTTCAAGGAAAATTGATCTTTC
Found at i:1394168 original size:57 final size:58
Alignment explanation
Indices: 1394060--1394341 Score: 286
Period size: 59 Copynumber: 4.8 Consensus size: 58
1394050 TTGTATAGGA
* * *
1394060 GAAAATTGATACTTTTAACTTTTTCC-CTAAA-AATTTTTTTGGAAACTTTAAT-TTCAAG
1 GAAAATTGATACTTTCAAC-TTTTCCTCAAAATAATTTTTTT-GAAAATTT-ATCTTCAAG
* *
1394118 GAAAATTGATACTTTCAACTTTTCCTCAAAA-AATTTTTTTGAAACTTTAAT-TTCGAG
1 GAAAATTGATACTTTCAACTTTTCCTCAAAATAATTTTTTTGAAAATTT-ATCTTCAAG
* ** * *
1394175 GAAAATTGATGCTTTCAACTTTTCCTCAAAACTTTTTTTTTTTAAAATTTATCTTTAAG
1 GAAAATTGATACTTTCAACTTTTCCTCAAAA-TAATTTTTTTGAAAATTTATCTTCAAG
* * ** *
1394234 AAAAATTGATACTTTCAACTTTTCGTCAAAACCTTTTTTTTTTTTTGAAAATTTATCTTTAAG
1 GAAAATTGATACTTTCAACTTTTCCTCAAAA-----TAATTTTTTTGAAAATTTATCTTCAAG
*
1394297 AAAAATTGATACTTTCAACTTTTCCTCAAAAATAATTTTTTTGAA
1 GAAAATTGATACTTTCAACTTTTCCTC-AAAATAATTTTTTTGAA
1394342 TTTTTTTTAA
Statistics
Matches: 197, Mismatches: 18, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
57 52 0.26
58 33 0.17
59 56 0.28
63 52 0.26
64 4 0.02
ACGTcount: A:0.34, C:0.13, G:0.07, T:0.46
Consensus pattern (58 bp):
GAAAATTGATACTTTCAACTTTTCCTCAAAATAATTTTTTTGAAAATTTATCTTCAAG
Found at i:1394302 original size:63 final size:59
Alignment explanation
Indices: 1394119--1394327 Score: 271
Period size: 63 Copynumber: 3.5 Consensus size: 59
1394109 AATTTCAAGG
** * * ** *
1394119 AAAATTGATACTTTCAACTTTTCCTCAAAA--AATTTTTTTGAAACTTTAAT-TTCGAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAACTTTTTTTTTTTAAAATTT-ATCTTTAAGA
*
1394176 AAAATTGATGCTTTCAACTTTTCCTCAAAACTTTTTTTTTTTAAAATTTATCTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAACTTTTTTTTTTTAAAATTTATCTTTAAGA
*
1394235 AAAATTGATACTTTCAACTTTTCGTCAAAACCTTTTTTTTTTTTTGAAAATTTATCTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAA-C--TTTTTTTTTTT-AAAATTTATCTTTAAGA
1394298 AAAATTGATACTTTCAACTTTTCCTCAAAA
1 AAAATTGATACTTTCAACTTTTCCTCAAAA
1394328 ATAATTTTTT
Statistics
Matches: 134, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
57 29 0.22
58 2 0.01
59 45 0.34
60 1 0.01
62 11 0.08
63 46 0.34
ACGTcount: A:0.34, C:0.14, G:0.06, T:0.45
Consensus pattern (59 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAACTTTTTTTTTTTAAAATTTATCTTTAAGA
Found at i:1394336 original size:63 final size:61
Alignment explanation
Indices: 1394061--1394338 Score: 274
Period size: 57 Copynumber: 4.7 Consensus size: 61
1394051 TGTATAGGAG
* * * * *
1394061 AAAATTGATACTTTTAACTTTTTCC-CTAAAAA---TTTTTTTGGAAACTTTAATTTCAAGG
1 AAAATTGATACTTTCAAC-TTTTCCTCAAAAAATTTTTTTTTTTGAAAATTTAATTTCAAGA
* * *
1394119 AAAATTGATACTTTCAACTTTTCCTCAAAAAA----TTTTTTTGAAACTTTAATTTCGAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAAATTTTTTTTTTTGAAAATTTAATTTCAAGA
* * *
1394176 AAAATTGATGCTTTCAACTTTTCCTC-AAAACTTTTTTTTTTT-AAAATTT-ATCTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAAATTTTTTTTTTTGAAAATTTAAT-TTCAAGA
* ** *
1394235 AAAATTGATACTTTCAACTTTTCGTCAAAACCTTTTTTTTTTTTTGAAAATTT-ATCTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAA--AATTTTTTTTTTTGAAAATTTAAT-TTCAAGA
*
1394298 AAAATTGATACTTTCAACTTTTCCTCAAAAATAATTTTTTT
1 AAAATTGATACTTTCAACTTTTCCTCAAAAA-ATTTTTTTT
1394339 GAATTTTTTT
Statistics
Matches: 191, Mismatches: 18, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
56 4 0.02
57 54 0.28
58 25 0.13
59 34 0.18
60 10 0.05
62 18 0.09
63 46 0.24
ACGTcount: A:0.34, C:0.13, G:0.06, T:0.46
Consensus pattern (61 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAAATTTTTTTTTTTGAAAATTTAATTTCAAGA
Found at i:1394367 original size:13 final size:13
Alignment explanation
Indices: 1394351--1394375 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1394341 ATTTTTTTTA
1394351 AAAATAAAATAAT
1 AAAATAAAATAAT
1394364 AAAATAAAATAA
1 AAAATAAAATAA
1394376 ACAAAGTAAA
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAATAAAATAAT
Found at i:1394408 original size:21 final size:20
Alignment explanation
Indices: 1394351--1394411 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 20
1394341 ATTTTTTTTA
1394351 AAAATAAAAT-AAT-AAAAT
1 AAAATAAAATAAATAAAAAT
*
1394369 AAAATAAACA-AAGTAAAAAT
1 AAAATAAA-ATAAATAAAAAT
*
1394389 GAAAATAAATAAAAATAAAAAT
1 -AAAATAAA-ATAAATAAAAAT
1394411 A
1 A
1394412 TTAAACAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
18 8 0.23
19 3 0.09
20 5 0.14
21 10 0.29
22 9 0.26
ACGTcount: A:0.77, C:0.02, G:0.03, T:0.18
Consensus pattern (20 bp):
AAAATAAAATAAATAAAAAT
Found at i:1394893 original size:19 final size:19
Alignment explanation
Indices: 1394869--1394912 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1394859 AGAAATATTA
1394869 TCGAAAA-TTGAAAAGTTGG
1 TCGAAAACTT-AAAAGTTGG
*
1394888 TCGAAAACTTCAAAGTTGG
1 TCGAAAACTTAAAAGTTGG
*
1394907 CCGAAA
1 TCGAAA
1394913 TAGCTGCTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 20 0.91
20 2 0.09
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.23
Consensus pattern (19 bp):
TCGAAAACTTAAAAGTTGG
Found at i:1395323 original size:19 final size:19
Alignment explanation
Indices: 1395301--1395337 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1395291 AAAAAATCAG
1395301 AAAAATAAAAAATTAAATA
1 AAAAATAAAAAATTAAATA
* *
1395320 AAAAATATATAATTAAAT
1 AAAAATAAAAAATTAAAT
1395338 GAAGATAATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAAATAAAAAATTAAATA
Found at i:1395373 original size:20 final size:21
Alignment explanation
Indices: 1395342--1395431 Score: 80
Period size: 21 Copynumber: 4.1 Consensus size: 21
1395332 TTAAATGAAG
1395342 ATAATCAGATAAA-CAAAAA-A
1 ATAAT-AGATAAATCAAAAATA
*
1395362 ATTAATAGATAAATTAAAAATA
1 A-TAATAGATAAATCAAAAATA
1395384 ATAATAGATAAATAACAATAAATA
1 ATAATAGATAAAT--CAA-AAATA
1395408 TATAACTAGATAAAT-AAAAA-A
1 -ATAA-TAGATAAATCAAAAATA
1395429 ATA
1 ATA
1395432 TATATGAATA
Statistics
Matches: 60, Mismatches: 2, Indels: 16
0.77 0.03 0.21
Matches are distributed among these distances:
20 11 0.18
21 22 0.37
22 5 0.08
23 4 0.07
24 5 0.08
25 4 0.07
26 9 0.15
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.24
Consensus pattern (21 bp):
ATAATAGATAAATCAAAAATA
Found at i:1395434 original size:26 final size:25
Alignment explanation
Indices: 1395353--1395441 Score: 84
Period size: 26 Copynumber: 3.7 Consensus size: 25
1395343 TAATCAGATA
1395353 AACAAAAAA-AT-TAATAGATAAAT
1 AACAAAAAATATATAATAGATAAAT
*
1395376 ---TAAAAATA-ATAATAGATAAAT
1 AACAAAAAATATATAATAGATAAAT
*
1395397 AACAATAAATATATAACTAGATAAAT
1 AACAAAAAATATATAA-TAGATAAAT
1395423 AA-AAAAATATATATGAATA
1 AACAAAAA-ATATAT-AATA
1395442 TTAACAGAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 15
0.74 0.06 0.21
Matches are distributed among these distances:
20 5 0.09
21 13 0.25
24 6 0.11
25 8 0.15
26 19 0.36
27 2 0.04
ACGTcount: A:0.66, C:0.03, G:0.04, T:0.26
Consensus pattern (25 bp):
AACAAAAAATATATAATAGATAAAT
Found at i:1395481 original size:14 final size:15
Alignment explanation
Indices: 1395447--1395480 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
1395437 GAATATTAAC
1395447 AGAAAAGAAAGAAAA
1 AGAAAAGAAAGAAAA
1395462 AGAAAAG-AAG-AAA
1 AGAAAAGAAAGAAAA
1395475 AGAAAA
1 AGAAAA
1395481 AAAATAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.47
14 3 0.16
15 7 0.37
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
AGAAAAGAAAGAAAA
Found at i:1395490 original size:18 final size:18
Alignment explanation
Indices: 1395449--1395490 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
1395439 ATATTAACAG
1395449 AAAAG-AAAGAAAAAGAA
1 AAAAGAAAAGAAAAAGAA
1395466 AAGAAGAAAAGAAAAA-AA
1 AA-AAGAAAAGAAAAAGAA
1395484 ATAAAGA
1 A-AAAGA
1395491 TATATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 2 0.09
18 10 0.45
19 10 0.45
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (18 bp):
AAAAGAAAAGAAAAAGAA
Found at i:1395585 original size:49 final size:47
Alignment explanation
Indices: 1395478--1395587 Score: 125
Period size: 48 Copynumber: 2.3 Consensus size: 47
1395468 GAAGAAAAGA
* *
1395478 AAAAAAATAAAGATATATATATATTAATAAATAGTAATAATAAATAC
1 AAAAAAATAAAAATATATATATATAAATAAATAGTAATAATAAATAC
* *
1395525 ATAAAAGATAAAAATGTATATATATAATATAAATA-TAA-ATATAAAATAC
1 A-AAAAAATAAAAATATATATATATAA-ATAAATAGTAATA-AT-AAATAC
1395574 AAAAATAATAAAAA
1 AAAAA-AATAAAAA
1395588 AAATAAAGTG
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
47 2 0.04
48 30 0.57
49 21 0.40
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (47 bp):
AAAAAAATAAAAATATATATATATAAATAAATAGTAATAATAAATAC
Found at i:1395932 original size:43 final size:43
Alignment explanation
Indices: 1395775--1395964 Score: 188
Period size: 43 Copynumber: 4.4 Consensus size: 43
1395765 TTTGATCAAG
* *
1395775 GCTCCTCTAAGCAGAGACTCAATGACTTTGAAAAATATAA-ACAA
1 GCTCCTCTAAACAGAGGCTCAATGACTTTGAAAAATA-AATA-AA
* *
1395819 TGTTCCTCTAATCAGAGGCTCAATGACTTT-AAAAATAAATAAA
1 -GCTCCTCTAAACAGAGGCTCAATGACTTTGAAAAATAAATAAA
* * ** * * *
1395862 GCTCATTTAATTAAAGACTCAACGACTTTGAAAAATAAATAAA
1 GCTCCTCTAAACAGAGGCTCAATGACTTTGAAAAATAAATAAA
* * *
1395905 ACTCCTCTAAACAGAGGTTCAATGACTTTTG-AAAATAAACAAA
1 GCTCCTCTAAACAGAGGCTCAATGAC-TTTGAAAAATAAATAAA
*
1395948 GCTCCTCTAAATAGAGG
1 GCTCCTCTAAACAGAGG
1395965 TAATTTTTTT
Statistics
Matches: 120, Mismatches: 22, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
42 22 0.18
43 60 0.50
44 12 0.10
45 26 0.22
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Consensus pattern (43 bp):
GCTCCTCTAAACAGAGGCTCAATGACTTTGAAAAATAAATAAA
Found at i:1395991 original size:19 final size:19
Alignment explanation
Indices: 1395967--1396003 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1395957 AATAGAGGTA
*
1395967 ATTTTTTTGTTTTTTTTTT
1 ATTTTTTTATTTTTTTTTT
1395986 ATTTTTTTATTTTTTTTT
1 ATTTTTTTATTTTTTTTT
1396004 ATAAAGCTCA
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:0.08, C:0.00, G:0.03, T:0.89
Consensus pattern (19 bp):
ATTTTTTTATTTTTTTTTT
Found at i:1395992 original size:18 final size:18
Alignment explanation
Indices: 1395967--1396005 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
1395957 AATAGAGGTA
*
1395967 ATTTTTTTGTTTTTTTTTT
1 ATTTTTTT-ATTTTTTTTT
1395986 ATTTTTTTATTTTTTTTT
1 ATTTTTTTATTTTTTTTT
1396004 AT
1 AT
1396006 AAAGCTCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.10, C:0.00, G:0.03, T:0.87
Consensus pattern (18 bp):
ATTTTTTTATTTTTTTTT
Found at i:1396004 original size:10 final size:10
Alignment explanation
Indices: 1395968--1396005 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1395958 ATAGAGGTAA
*
1395968 TTTTTTTGTT
1 TTTTTTTATT
*
1395978 TTTTTTT-TA
1 TTTTTTTATT
1395987 TTTTTTTATT
1 TTTTTTTATT
1395997 TTTTTTTAT
1 TTTTTTTAT
1396006 AAAGCTCATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 8 0.32
10 17 0.68
ACGTcount: A:0.08, C:0.00, G:0.03, T:0.89
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:1396119 original size:51 final size:49
Alignment explanation
Indices: 1396009--1396182 Score: 184
Period size: 51 Copynumber: 3.6 Consensus size: 49
1395999 TTTTTATAAA
* * ** *
1396009 GCTCATCTAAGCAGAGGCTCAACGAC-TCAATGACTTTGGAAAAATAAATA
1 GCTCATCTAATCAGAGGCTCAACAACTTTGA-GACTTT-GAAAAATAAATG
*
1396059 GCTCCTCTAATCAGAGGCTCAACAACTTTGACGACTTTGAAAAAATAAATG
1 GCTCATCTAATCAGAGGCTCAACAACTTTGA-GACTTTG-AAAAATAAATG
*
1396110 GCTCATCTAATTAGAGGCTCAACAACTTT--G-----GAAAAATAAATG
1 GCTCATCTAATCAGAGGCTCAACAACTTTGAGACTTTGAAAAATAAATG
*
1396152 GCTCCTCTAATCAGAGGCTCAACAACTTTGA
1 GCTCATCTAATCAGAGGCTCAACAACTTTGA
1396183 AAAGTAAAGG
Statistics
Matches: 109, Mismatches: 11, Indels: 14
0.81 0.08 0.10
Matches are distributed among these distances:
42 38 0.35
43 1 0.01
48 1 0.01
50 24 0.22
51 45 0.41
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (49 bp):
GCTCATCTAATCAGAGGCTCAACAACTTTGAGACTTTGAAAAATAAATG
Found at i:1396151 original size:42 final size:41
Alignment explanation
Indices: 1396092--1396444 Score: 340
Period size: 41 Copynumber: 8.5 Consensus size: 41
1396082 AACTTTGACG
* * * *
1396092 ACTTTGAAAAAATAAATGGCTCATCTAATTAGAGGCTCAACA
1 ACTTTG-AAAAGTAAATTGCTCCTCTAAATAGAGGCTCAACA
* *
1396134 ACTTTGGAAAAATAAATGGCTCCTCT-AATCAGAGGCTCAACA
1 ACTTT-GAAAAGTAAATTGCTCCTCTAAAT-AGAGGCTCAACA
**
1396176 ACTTTGAAAAGTAAAGGGCTCCTCT-AATCAGAGGCTCAACA
1 ACTTTGAAAAGTAAATTGCTCCTCTAAAT-AGAGGCTCAACA
* * * *
1396217 ACTTTGAAAAGTAAATTGCTCATCTAAATGGAGGCACCACA
1 ACTTTGAAAAGTAAATTGCTCCTCTAAATAGAGGCTCAACA
* * *
1396258 ACTTTGAAAAGTAAATTGCTCCTTTAAATAGAGGCAACCACA
1 ACTTTGAAAAGTAAATTGCTCCTCTAAATAGAGGC-TCAACA
* * * *
1396300 ACTTTGGAAAGTAAATTGCTCTTCTAAACAGAGGCAATC-ACG
1 ACTTTGAAAAGTAAATTGCTCCTCTAAATAGAGGC--TCAACA
* * *
1396342 ACTTTGAAAAATAAATTGCTCTTCTAAATAGAGGCAACAA-A
1 ACTTTGAAAAGTAAATTGCTCCTCTAAATAGAGGC-TCAACA
* *
1396383 ACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGG--CAACGAA
1 ACTTTGAAAAGTAAATTGCTCCTCTAAATAGAGGCTCAAC--A
* *
1396424 ACTTCGAAAAGTAAATGGCTC
1 ACTTTGAAAAGTAAATTGCTC
1396445 ATTGACAATC
Statistics
Matches: 271, Mismatches: 31, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
38 3 0.01
41 150 0.55
42 115 0.42
43 3 0.01
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.25
Consensus pattern (41 bp):
ACTTTGAAAAGTAAATTGCTCCTCTAAATAGAGGCTCAACA
Found at i:1396209 original size:83 final size:83
Alignment explanation
Indices: 1396092--1396444 Score: 378
Period size: 83 Copynumber: 4.3 Consensus size: 83
1396082 AACTTTGACG
* * * * * *
1396092 ACTTTGAAAAAATAAATGGCTCATCTAATTAGAGGC-TCAACAACTTTGGAAAAATAAATGGCTC
1 ACTTTG-AAAAGTAAATGGCTCCTCTAAATAGAGGCAACAACAACTTTGG-AAAGTAAATTGCTC
*
1396156 CTCTAATCAGAGGCTCAACA
64 CTCTAAACAGAGGCTCAACA
* * * *
1396176 ACTTTGAAAAGTAAAGGGCTCCTCT-AATCAGAGGC-TCAACAACTTTGAAAAGTAAATTGCTCA
1 ACTTTGAAAAGTAAATGGCTCCTCTAAAT-AGAGGCAACAACAACTTTGGAAAGTAAATTGCTCC
** * *
1396239 TCTAAATGGAGGCACCACA
65 TCTAAACAGAGGCTCAACA
* * * *
1396258 ACTTTGAAAAGTAAATTGCTCCTTTAAATAGAGGCAACCACAACTTTGGAAAGTAAATTGCTCTT
1 ACTTTGAAAAGTAAATGGCTCCTCTAAATAGAGGCAACAACAACTTTGGAAAGTAAATTGCTCCT
*
1396323 CTAAACAGAGGCAATC-ACG
66 CTAAACAGAGGC--TCAACA
* * *
1396342 ACTTTGAAAAATAAATTGCTCTTCTAAATAGAGGCAACAA-AACTTTGGAAAGTAAATTGCTCCT
1 ACTTTGAAAAGTAAATGGCTCCTCTAAATAGAGGCAACAACAACTTTGGAAAGTAAATTGCTCCT
1396406 CTAAACAGAGG--CAACGAA
66 CTAAACAGAGGCTCAAC--A
*
1396424 ACTTCGAAAAGTAAATGGCTC
1 ACTTTGAAAAGTAAATGGCTC
1396445 ATTGACAATC
Statistics
Matches: 228, Mismatches: 33, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
79 1 0.00
80 2 0.01
82 74 0.32
83 106 0.46
84 44 0.19
85 1 0.00
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.25
Consensus pattern (83 bp):
ACTTTGAAAAGTAAATGGCTCCTCTAAATAGAGGCAACAACAACTTTGGAAAGTAAATTGCTCCT
CTAAACAGAGGCTCAACA
Found at i:1398342 original size:11 final size:11
Alignment explanation
Indices: 1398326--1398399 Score: 63
Period size: 11 Copynumber: 7.2 Consensus size: 11
1398316 CTTTTTTTCA
1398326 TTTTCTCATTT
1 TTTTCTCATTT
*
1398337 TTTTCTTATTT
1 TTTTCTCATTT
*
1398348 TTTTCTTA-TT
1 TTTTCTCATTT
1398358 TTTT-T-A-TT
1 TTTTCTCATTT
1398366 TTTTCATCATCTT
1 TTTTC-TCAT-TT
1398379 TTTT-TC--TT
1 TTTTCTCATTT
1398387 TTTTCTCATTT
1 TTTTCTCATTT
1398398 TT
1 TT
1398400 CACCCATTGT
Statistics
Matches: 54, Mismatches: 1, Indels: 16
0.76 0.01 0.23
Matches are distributed among these distances:
8 13 0.24
9 3 0.06
10 7 0.13
11 25 0.46
13 6 0.11
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTCTCATTT
Found at i:1398351 original size:12 final size:11
Alignment explanation
Indices: 1398326--1398362 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
1398316 CTTTTTTTCA
*
1398326 TTTTCTCATTT
1 TTTTCTTATTT
1398337 TTTTCTTATTT
1 TTTTCTTATTT
1398348 TTTTCTTATTT
1 TTTTCTTATTT
1398359 TTTT
1 TTTT
1398363 ATTTTTTCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTCTTATTT
Found at i:1398400 original size:30 final size:30
Alignment explanation
Indices: 1398314--1398401 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 30
1398304 CAATTTGAAT
* *
1398314 ATCTTTTTTTC-ATTTTCTCATTTTT-TTC
1 ATCTTTTTTTCTTTTTTCTCATTTTTCATC
* * * *
1398342 TTATTTTTTTCTTATTTTTTTATTTTTTCATC
1 ATCTTTTTTTCTT-TTTTCTCA-TTTTTCATC
1398374 ATCTTTTTTTCTTTTTTCTCATTTTTCA
1 ATCTTTTTTTCTTTTTTCTCATTTTTCA
1398402 CCCATTGTTG
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
28 9 0.20
30 13 0.28
31 11 0.24
32 13 0.28
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (30 bp):
ATCTTTTTTTCTTTTTTCTCATTTTTCATC
Found at i:1403234 original size:27 final size:27
Alignment explanation
Indices: 1403204--1403293 Score: 65
Period size: 27 Copynumber: 3.2 Consensus size: 27
1403194 TTGTACAGGA
1403204 AAAAATTGATACTTTCAACTTTTTCTC
1 AAAAATTGATACTTTCAACTTTTTCTC
* * ** * * * *
1403231 AAAACTT-TTTTTTTTAAATTTATCTTTA
1 AAAAATTGATACTTTCAACTTT-T-TCTC
1403259 AGAAAAATTGATACTTTCAACTTTTTCTC
1 A--AAAATTGATACTTTCAACTTTTTCTC
1403288 AAAAAT
1 AAAAAT
1403294 AATTTTTTTT
Statistics
Matches: 42, Mismatches: 16, Indels: 10
0.62 0.24 0.15
Matches are distributed among these distances:
26 9 0.21
27 12 0.29
28 3 0.07
29 3 0.07
30 6 0.14
31 9 0.21
ACGTcount: A:0.37, C:0.13, G:0.03, T:0.47
Consensus pattern (27 bp):
AAAAATTGATACTTTCAACTTTTTCTC
Found at i:1403357 original size:10 final size:10
Alignment explanation
Indices: 1403339--1403383 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
1403329 AACAAAGTAA
*
1403339 AAATGAAAAT
1 AAATAAAAAT
1403349 AAATAAAAAGAT
1 AAAT-AAAA-AT
1403361 AAATAAAAAT
1 AAATAAAAAT
*
1403371 AAATACAAAT
1 AAATAAAAAT
1403381 AAA
1 AAA
1403384 AATATTAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 18 0.58
11 7 0.23
12 6 0.19
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:1403386 original size:22 final size:22
Alignment explanation
Indices: 1403317--1403387 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 22
1403307 AATTTTTTTA
1403317 AAAAAT-AAAAT-AA-ACAAAGT
1 AAAAATAAAAATAAATACAAA-T
* * *
1403337 AAAAATGAAAATAAATAAAAAG
1 AAAAATAAAAATAAATACAAAT
*
1403359 ATAAATAAAAATAAATACAAAT
1 AAAAATAAAAATAAATACAAAT
1403381 AAAAATA
1 AAAAATA
1403388 TTAAACCATT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
20 6 0.15
21 5 0.12
22 26 0.63
23 4 0.10
ACGTcount: A:0.76, C:0.03, G:0.04, T:0.17
Consensus pattern (22 bp):
AAAAATAAAAATAAATACAAAT
Found at i:1404217 original size:19 final size:19
Alignment explanation
Indices: 1404195--1404232 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1404185 AAAAAAATCA
1404195 AAAAAATAAAAAATTAAAT
1 AAAAAATAAAAAATTAAAT
* *
1404214 AAAAAATATATAATTAAAT
1 AAAAAATAAAAAATTAAAT
1404233 GAAGATAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (19 bp):
AAAAAATAAAAAATTAAAT
Found at i:1404292 original size:14 final size:14
Alignment explanation
Indices: 1404275--1404319 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
1404265 ATAAATTAAC
1404275 AATAATAATAGATA
1 AATAATAATAGATA
1404289 AATAATAATA-A-A
1 AATAATAATAGATA
*
1404301 CAT-ATAACTAGATA
1 AATAATAA-TAGATA
1404315 AATAA
1 AATAA
1404320 ATATATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
11 4 0.16
12 5 0.20
13 2 0.08
14 13 0.52
15 1 0.04
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.27
Consensus pattern (14 bp):
AATAATAATAGATA
Found at i:1404358 original size:9 final size:9
Alignment explanation
Indices: 1404344--1404380 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
1404334 GAATATTAAC
1404344 AGAAAAAAA
1 AGAAAAAAA
1404353 AGAAAAAAA
1 AGAAAAAAA
1404362 A-AGAAAAAA
1 AGA-AAAAAA
1404371 AGAAAAAAA
1 AGAAAAAAA
1404380 A
1 A
1404381 ATAAAGATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 1 0.04
9 24 0.92
10 1 0.04
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (9 bp):
AGAAAAAAA
Found at i:1404361 original size:10 final size:10
Alignment explanation
Indices: 1404346--1404381 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
1404336 ATATTAACAG
1404346 AAAAAAAAGA
1 AAAAAAAAGA
1404356 AAAAAAAAG-
1 AAAAAAAAGA
1404365 -AAAAAAAGA
1 AAAAAAAAGA
1404374 AAAAAAAA
1 AAAAAAAA
1404382 TAAAGATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 8 0.33
10 16 0.67
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:1404370 original size:18 final size:18
Alignment explanation
Indices: 1404347--1404381 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1404337 TATTAACAGA
1404347 AAAAAAAGAAAAAAAAAG
1 AAAAAAAGAAAAAAAAAG
1404365 AAAAAAAGAAAAAAAAA
1 AAAAAAAGAAAAAAAAA
1404382 TAAAGATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (18 bp):
AAAAAAAGAAAAAAAAAG
Found at i:1404429 original size:7 final size:7
Alignment explanation
Indices: 1404395--1404508 Score: 75
Period size: 7 Copynumber: 16.4 Consensus size: 7
1404385 AGATATATAT
1404395 TAATAAA
1 TAATAAA
*
1404402 TAGT-AA
1 TAATAAA
1404408 TAATAAA
1 TAATAAA
1404415 TAAGTAAA
1 TAA-TAAA
1404423 TAATAAA
1 TAATAAA
1404430 TACATAAA
1 TA-ATAAA
1404438 -AGATAAA
1 TA-ATAAA
1404445 TATATATAA
1 TA-ATA-AA
1404454 T-ATAAA
1 TAATAAA
1404460 -ATATAAA
1 TA-ATAAA
1404467 T-ATAAA
1 TAATAAA
1404473 T-ATAAA
1 TAATAAA
1404479 T-ATAAAA
1 TAAT-AAA
*
1404486 TAAAAAAA
1 T-AATAAA
1404494 TAATAAA
1 TAATAAA
1404501 -AA-AAA
1 TAATAAA
1404506 TAA
1 TAA
1404509 AATGGACCAA
Statistics
Matches: 89, Mismatches: 6, Indels: 25
0.74 0.05 0.21
Matches are distributed among these distances:
5 3 0.03
6 25 0.28
7 37 0.42
8 20 0.22
9 4 0.04
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (7 bp):
TAATAAA
Found at i:1404437 original size:15 final size:14
Alignment explanation
Indices: 1404395--1404508 Score: 75
Period size: 15 Copynumber: 8.2 Consensus size: 14
1404385 AGATATATAT
*
1404395 TAATAAATAGT-AA
1 TAATAAATAATAAA
1404408 TAATAAATAAGTAAA
1 TAATAAATAA-TAAA
1404423 TAATAAATACATAAA
1 TAATAAATA-ATAAA
1404438 -AGATAAATATATATAA
1 TA-ATAAATA-ATA-AA
1404454 T-ATAAA-ATATAAA
1 TAATAAATA-ATAAA
1404467 T-ATAAAT-ATAAA
1 TAATAAATAATAAA
*
1404479 T-ATAAAATAAAAAAA
1 TAAT-AAAT-AATAAA
1404494 TAATAAA-AA-AAA
1 TAATAAATAATAAA
1404506 TAA
1 TAA
1404509 AATGGACCAA
Statistics
Matches: 87, Mismatches: 3, Indels: 23
0.77 0.03 0.20
Matches are distributed among these distances:
12 14 0.16
13 23 0.26
14 7 0.08
15 38 0.44
16 5 0.06
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (14 bp):
TAATAAATAATAAA
Found at i:1404444 original size:22 final size:21
Alignment explanation
Indices: 1404397--1404508 Score: 69
Period size: 22 Copynumber: 5.4 Consensus size: 21
1404387 ATATATATTA
*
1404397 ATAAATAGT-AATAATAAATA-
1 ATAAATAATAAATAATAAA-AG
1404417 AGTAAATAATAAATACATAAAAG
1 A-TAAATAATAAATA-ATAAAAG
*
1404440 ATAAATATATATAAT-ATAAAAT
1 ATAAATA-ATA-AATAATAAAAG
*
1404462 ATAAAT-ATAAAT-AT-AAAT
1 ATAAATAATAAATAATAAAAG
*
1404480 ATAAAATAAAAAAATAATAAAA-
1 AT-AAAT-AATAAATAATAAAAG
1404502 A-AAATAA
1 ATAAATAA
1404509 AATGGACCAA
Statistics
Matches: 78, Mismatches: 3, Indels: 23
0.75 0.03 0.22
Matches are distributed among these distances:
18 6 0.08
19 11 0.14
20 8 0.10
21 12 0.15
22 26 0.33
23 12 0.15
24 3 0.04
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.27
Consensus pattern (21 bp):
ATAAATAATAAATAATAAAAG
Found at i:1404453 original size:28 final size:26
Alignment explanation
Indices: 1404377--1404509 Score: 85
Period size: 28 Copynumber: 4.8 Consensus size: 26
1404367 AAAAAGAAAA
* *
1404377 AAAAATAAAGATATATATTAATAAATAGT
1 AAAAAT-AA-ATATA-AATAATAAATAAT
*
1404406 AATAATAAATAAGTAAATAATAAATACAT
1 AAAAATAAAT-A-TAAATAATAAATA-AT
*
1404435 AAAAGATAAATATATATAATATAA-AAT
1 AAAA-ATAAATATAAATAATA-AATAAT
1404462 ATAAATATAAATATAAAT-ATAAAATAA-
1 A-AAA-ATAAATATAAATAAT-AAATAAT
* *
1404489 AAAAAT-AATAAAAAAAATAAA
1 AAAAATAAATATAAATAATAAA
1404510 ATGGACCAAC
Statistics
Matches: 86, Mismatches: 9, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
24 10 0.12
25 4 0.05
26 3 0.03
27 10 0.12
28 39 0.45
29 14 0.16
30 6 0.07
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (26 bp):
AAAAATAAATATAAATAATAAATAAT
Found at i:1404469 original size:6 final size:6
Alignment explanation
Indices: 1404446--1404489 Score: 63
Period size: 6 Copynumber: 7.2 Consensus size: 6
1404436 AAAGATAAAT
1404446 ATATATA ATATAAA ATATAA ATATAA ATATAA ATATAA A-ATAA A
1 ATATA-A ATAT-AA ATATAA ATATAA ATATAA ATATAA ATATAA A
1404490 AAAATAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.14
6 21 0.58
7 9 0.25
8 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
ATATAA
Found at i:1404471 original size:18 final size:17
Alignment explanation
Indices: 1404448--1404511 Score: 71
Period size: 18 Copynumber: 3.8 Consensus size: 17
1404438 AGATAAATAT
1404448 ATATAATATAAAATATAA
1 ATATAA-ATAAAATATAA
1404466 ATATAAATATAAATATAA
1 ATATAAATA-AAATATAA
1404484 A-ATAAA-AAAATAATAA
1 ATATAAATAAAAT-ATAA
*
1404500 A-AAAAATAAAAT
1 ATATAAATAAAAT
1404512 GGACCAACCC
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
15 4 0.10
16 10 0.24
17 13 0.31
18 15 0.36
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
ATATAAATAAAATATAA
Found at i:1413523 original size:2 final size:2
Alignment explanation
Indices: 1413516--1413543 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1413506 CATCCAAAAC
1413516 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
1413544 GTTTCCCCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1414545 original size:20 final size:20
Alignment explanation
Indices: 1414520--1414557 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1414510 ACATACATAC
1414520 ATATATATATATATGTATGT
1 ATATATATATATATGTATGT
*
1414540 ATATATTTATATATGTAT
1 ATATATATATATATGTAT
1414558 ACATGTATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (20 bp):
ATATATATATATATGTATGT
Found at i:1414563 original size:8 final size:8
Alignment explanation
Indices: 1414523--1414565 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
1414513 TACATACATA
*
1414523 TATATATA
1 TATATATG
*
1414531 TATGTATG
1 TATATATG
*
1414539 TATATATT
1 TATATATG
1414547 TATATATG
1 TATATATG
*
1414555 TATACATG
1 TATATATG
1414563 TAT
1 TAT
1414566 GCATTAATGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.51
Consensus pattern (8 bp):
TATATATG
Found at i:1417682 original size:22 final size:21
Alignment explanation
Indices: 1417665--1417706 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1417655 GTAACATTAT
*
1417665 AGCTGAAATCATGCAACACAAC
1 AGCTGAAAT-ATGCAACATAAC
1417687 AGCTGAAATATGCAACATAA
1 AGCTGAAATATGCAACATAA
1417707 TTTTAACTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (21 bp):
AGCTGAAATATGCAACATAAC
Found at i:1418856 original size:15 final size:15
Alignment explanation
Indices: 1418836--1418867 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1418826 GAAAAAGTAA
*
1418836 TTAATAGATAACTTT
1 TTAATAGATAAATTT
1418851 TTAATAGATAAATTT
1 TTAATAGATAAATTT
1418866 TT
1 TT
1418868 CATATTTTAA
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:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (15 bp):
TTAATAGATAAATTT
Found at i:1424042 original size:27 final size:27
Alignment explanation
Indices: 1424012--1424082 Score: 133
Period size: 27 Copynumber: 2.6 Consensus size: 27
1424002 TCCTTGGTCT
*
1424012 AAACGACGTCGTTTTGGGCGTTTATTG
1 AAACGACGTCGTTTTGGACGTTTATTG
1424039 AAACGACGTCGTTTTGGACGTTTATTG
1 AAACGACGTCGTTTTGGACGTTTATTG
1424066 AAACGACGTCGTTTTGG
1 AAACGACGTCGTTTTGG
1424083 CTATTGACAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.21, C:0.15, G:0.28, T:0.35
Consensus pattern (27 bp):
AAACGACGTCGTTTTGGACGTTTATTG
Found at i:1424851 original size:19 final size:19
Alignment explanation
Indices: 1424829--1424876 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
1424819 TTTATTTTTT
*
1424829 TTTCGTATTTTTTA-TATTA
1 TTTCATATTTTTTATTA-TA
1424848 TTTCATA-TTTTTATTATA
1 TTTCATATTTTTTATTATA
1424866 TTTCATATTTT
1 TTTCATATTTT
1424877 ACACATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 15 0.58
19 11 0.42
ACGTcount: A:0.23, C:0.06, G:0.02, T:0.69
Consensus pattern (19 bp):
TTTCATATTTTTTATTATA
Found at i:1425204 original size:97 final size:96
Alignment explanation
Indices: 1425052--1425553 Score: 647
Period size: 97 Copynumber: 5.2 Consensus size: 96
1425042 TGAAGCTCGG
* * * * *
1425052 CAACTTTAAAAATTTTATCTTGAAAATGGCTCCTCTCAGTAGAGGCTCTACAACTTTAAAAATCT
1 CAACTTT-AAAATCTCAT-TTGAAAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAATCT
* * *
1425117 CTTTTGGAAAA-GCTCCTCTCAGTAGAGGCTCAA
63 CATTTGAAAAAGGCTCCTCTCAGCAGAGGCTCAA
* * *
1425150 CAACTTTAAAATCTCATTTGAAAAAGGGCTCCTCTTAGCAAAAGCTCAACAACTTTAAAAT-TGC
1 CAACTTTAAAATCTCATTTGAAAAA-GGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCT-C
1425214 ATTTGAAAAAGGGCTCCTCTCAGCAGAGGCTCAA
64 ATTTGAAAAA-GGCTCCTCTCAGCAGAGGCTCAA
* * * *
1425248 CAACTTTAAAATCTCATTT-AAAAAAGCTCATCTCAGCAGTGGCTCAATAACTTTAAAATCTCAT
1 CAACTTTAAAATCTCATTTGAAAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCAT
1425312 CTTGAAAAAGGGCTCCTCTCAGCAGAGGCTCAA
66 -TTGAAAAA-GGCTCCTCTCAGCAGAGGCTCAA
* * *
1425345 CAATTTTAAAATCTCATTGGAAAAA-GCTCATCTCAGCAGAGGCTCAACAACTTTAAAATCTCAT
1 CAACTTTAAAATCTCATTTGAAAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCAT
*
1425409 TTGAAAAA-GCTCCTCTTAGCAGAGGCTCAA
66 TTGAAAAAGGCTCCTCTCAGCAGAGGCTCAA
* * * *
1425439 CAACTTTAAAATCTCATCTTGAAAAAGGGCTCCTCTTAACAAAGGCTCAACAACTTTAAAATTTC
1 CAACTTTAAAATCTCAT-TTGAAAAA-GGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTC
*
1425504 ATTGGAAAAA-GCTCCTCTCAGCAGAGGCTCAA
64 ATTTGAAAAAGGCTCCTCTCAGCAGAGGCTCAA
1425536 CAACTTTAAAAATCTCAT
1 CAACTTT-AAAATCTCAT
1425554 CTTCTCTCAA
Statistics
Matches: 361, Mismatches: 32, Indels: 22
0.87 0.08 0.05
Matches are distributed among these distances:
94 37 0.10
95 8 0.02
96 60 0.17
97 194 0.54
98 62 0.17
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (96 bp):
CAACTTTAAAATCTCATTTGAAAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCAT
TTGAAAAAGGCTCCTCTCAGCAGAGGCTCAA
Found at i:1425300 original size:47 final size:47
Alignment explanation
Indices: 1425080--1425553 Score: 572
Period size: 47 Copynumber: 9.8 Consensus size: 47
1425070 CTTGAAAATG
* * * **
1425080 GCTCCTCTCAGTAGAGGCTCTACAACTTTAAAAATCTCTTTTGGAAAA
1 GCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAATCTCATTTAAAAAA
* *
1425128 GCTCCTCTCAGTAGAGGCTCAACAACTTTAAAATCTCATTTGAAAAAGG
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATTT-AAAAA-A
* * * *
1425177 GCTCCTCTTAGCAAAAGCTCAACAACTTTAAAAT-TGCATTTGAAAAAGG
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCT-CATTT-AAAAA-A
1425226 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATTTAAAAAA
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATTTAAAAAA
* * * *
1425273 GCTCATCTCAGCAGTGGCTCAATAACTTTAAAATCTCATCTTGAAAAAGG
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCAT-TT-AAAAA-A
* **
1425323 GCTCCTCTCAGCAGAGGCTCAACAATTTTAAAATCTCATTGGAAAAA
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATTTAAAAAA
* *
1425370 GCTCATCTCAGCAGAGGCTCAACAACTTTAAAATCTCATTTGAAAAA
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATTTAAAAAA
* *
1425417 GCTCCTCTTAGCAGAGGCTCAACAACTTTAAAATCTCATCTTGAAAAAGG
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCAT-TT-AAAAA-A
* * * * **
1425467 GCTCCTCTTAACAAAGGCTCAACAACTTTAAAATTTCATTGGAAAAA
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATTTAAAAAA
1425514 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCAT
1 GCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAATCTCAT
1425554 CTTCTCTCAA
Statistics
Matches: 374, Mismatches: 41, Indels: 22
0.86 0.09 0.05
Matches are distributed among these distances:
47 154 0.41
48 58 0.16
49 90 0.24
50 72 0.19
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (47 bp):
GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATTTAAAAAA
Found at i:1425417 original size:144 final size:144
Alignment explanation
Indices: 1425080--1425553 Score: 729
Period size: 144 Copynumber: 3.3 Consensus size: 144
1425070 CTTGAAAATG
* * * * *
1425080 GCTCCTCTCAGTAGAGGCTCTACAACTTTAAAAATCTCTTTTGGAAAAGCTCCTCTCAGTAGAGG
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATTTGAAAAAGCTCCTCTCAGCAGAGG
*
1425145 CTCAACAACTTTAAAATCTCAT-TTGAAAAAGGGCTCCTCTTAGCAAAAGCTCAACAACTTTAAA
66 CTCAACAACTTTAAAATCTCATCTTGAAAAAGGGCTCCTCTTAGCAAAGGCTCAACAACTTTAAA
*
1425209 ATTGCATTTGAAAAA
131 ATT-CATTGGAAAAA
* * *
1425224 GGGCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAATCTCATTTAAAAAAGCTCATCTCAGCAGT
1 --GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATTTGAAAAAGCTCCTCTCAGCAGA
* * * *
1425288 GGCTCAATAACTTTAAAATCTCATCTTGAAAAAGGGCTCCTCTCAGCAGAGGCTCAACAATTTTA
64 GGCTCAACAACTTTAAAATCTCATCTTGAAAAAGGGCTCCTCTTAGCAAAGGCTCAACAACTTTA
1425353 AAATCTCATTGGAAAAA
129 AAAT-TCATTGGAAAAA
* *
1425370 GCTCATCTCAGCAGAGGCTCAACAACTTT-AAAATCTCATTTGAAAAAGCTCCTCTTAGCAGAGG
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATTTGAAAAAGCTCCTCTCAGCAGAGG
*
1425434 CTCAACAACTTTAAAATCTCATCTTGAAAAAGGGCTCCTCTTAACAAAGGCTCAACAACTTTAAA
66 CTCAACAACTTTAAAATCTCATCTTGAAAAAGGGCTCCTCTTAGCAAAGGCTCAACAACTTTAAA
1425499 ATTTCATTGGAAAAA
131 A-TTCATTGGAAAAA
1425514 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCAT
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCAT
1425554 CTTCTCTCAA
Statistics
Matches: 299, Mismatches: 25, Indels: 9
0.90 0.08 0.03
Matches are distributed among these distances:
144 160 0.54
145 61 0.20
146 77 0.26
147 1 0.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (144 bp):
GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATTTGAAAAAGCTCCTCTCAGCAGAGG
CTCAACAACTTTAAAATCTCATCTTGAAAAAGGGCTCCTCTTAGCAAAGGCTCAACAACTTTAAA
ATTCATTGGAAAAA
Found at i:1436142 original size:238 final size:236
Alignment explanation
Indices: 1435691--1436143 Score: 565
Period size: 238 Copynumber: 1.9 Consensus size: 236
1435681 TTATTGAAAT
* * *
1435691 TTTGAAGAAAAAAGAATTTAATTATATTGAAGATTTTCTATAAATATTATAATACGCTGGTAATA
1 TTTGAAGAAAAAAAAATTTAATTATATTGAAGATTTTCTATAAATATTACAATACACTGGTAATA
* * * * * *
1435756 TTTTATAAAAAATCTTCTCACGTAGAGATTTCTTAAAGCATCTCTATTCGGAATACTTTTAGAAT
66 TTTTACAAAAAATCTTCTCACGTAGAAATTTCGTAAAGCATCACTACTCGGAATACCTTTAGAAT
* * * * *
1435821 CTCATCATTGGATTAAATTTCTTTTCTTCTCATTTTTATTACTTATTTTTAATATATTAATCAAT
131 CTCATCATCGGATAAAATTTCTTTTCTCCTCATTTTTATTACTTAGTATTAATATATTAATCAAT
1435886 TTTTATTTATTATTTTTAAAAAAGAAATTTTTATTTAAAAA
196 TTTTATTTATTATTTTTAAAAAAGAAATTTTTATTTAAAAA
* * * *
1435927 TTTGAAGAAAAATGAAAATTTTATTATATTGAGGATTTTTTATAAATATTCCAATACACTGGTAA
1 TTTGAAGAAAAA--AAAATTTAATTATATTGAAGATTTTCTATAAATATTACAATACACTGGTAA
* * * *
1435992 TATTTTACAAAAAATCTTCTCACTTAGAAATTTCGT-AGGCATCACTGCTCGGATTACCTTT-GA
64 TATTTTACAAAAAATCTTCTCACGTAGAAATTTCGTAAAGCATCACTACTCGGAATACCTTTAGA
* *
1436055 ATCTCATCGTCGGATAAAATTTCTTTT-TCCTACATTTTTTATTAGTTTAGTATT-AT-TATTAA
129 ATCTCATCATCGGATAAAATTTCTTTTCTCCT-CA-TTTTTATTA-CTTAGTATTAATATATT-A
** *
1436117 ATTTATTTTTATATTATTGTTTTTAAA
190 ATCAATTTTTAT-TTATTATTTTTAAA
1436144 GTTTATTTTA
Statistics
Matches: 183, Mismatches: 27, Indels: 12
0.82 0.12 0.05
Matches are distributed among these distances:
235 3 0.02
236 44 0.24
237 41 0.22
238 95 0.52
ACGTcount: A:0.35, C:0.10, G:0.09, T:0.46
Consensus pattern (236 bp):
TTTGAAGAAAAAAAAATTTAATTATATTGAAGATTTTCTATAAATATTACAATACACTGGTAATA
TTTTACAAAAAATCTTCTCACGTAGAAATTTCGTAAAGCATCACTACTCGGAATACCTTTAGAAT
CTCATCATCGGATAAAATTTCTTTTCTCCTCATTTTTATTACTTAGTATTAATATATTAATCAAT
TTTTATTTATTATTTTTAAAAAAGAAATTTTTATTTAAAAA
Found at i:1437291 original size:19 final size:19
Alignment explanation
Indices: 1437269--1437316 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
1437259 TTATTTTTTT
*
1437269 TTTCGTATTTTTTA-TATTA
1 TTTCATATTTTTTATTA-TA
*
1437288 TTTCATA-TTTTTATTGTA
1 TTTCATATTTTTTATTATA
1437306 TTTCATATTTT
1 TTTCATATTTT
1437317 ATACATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.21, C:0.06, G:0.04, T:0.69
Consensus pattern (19 bp):
TTTCATATTTTTTATTATA
Found at i:1437300 original size:18 final size:18
Alignment explanation
Indices: 1437277--1437316 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
1437267 TTTTTCGTAT
1437277 TTTTTATAT-TATTTCATA
1 TTTTTAT-TGTATTTCATA
1437295 TTTTTATTGTATTTCATA
1 TTTTTATTGTATTTCATA
1437313 TTTT
1 TTTT
1437317 ATACATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 1 0.05
18 20 0.95
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.70
Consensus pattern (18 bp):
TTTTTATTGTATTTCATA
Found at i:1438392 original size:21 final size:20
Alignment explanation
Indices: 1438346--1438406 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 20
1438336 AGAATTTTGA
* *
1438346 ATTTTAAGGTTTGGGATTTGG
1 ATTTTAAGGTTAGGG-TTTCG
1438367 ATTTTAAGGTTAGGGTTTCG
1 ATTTTAAGGTTAGGGTTTCG
*
1438387 AGTTTTAGAGTTTAGGGTTT
1 A-TTTTA-AGGTTAGGGTTT
1438407 AGGTTTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.14
21 19 0.54
22 11 0.31
ACGTcount: A:0.20, C:0.02, G:0.31, T:0.48
Consensus pattern (20 bp):
ATTTTAAGGTTAGGGTTTCG
Found at i:1438414 original size:22 final size:21
Alignment explanation
Indices: 1438347--1438413 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
1438337 GAATTTTGAA
* *
1438347 TTTTAAGGTTTGGGATTTGGA-
1 TTTTAAGGTTAGGG-TTTAGAG
*
1438368 TTTTAAGGTTAGGGTTTCGAG
1 TTTTAAGGTTAGGGTTTAGAG
*
1438389 TTTTAGAGTTTAGGGTTTAG-G
1 TTTTA-AGGTTAGGGTTTAGAG
1438410 TTTT
1 TTTT
1438414 TTTTATTTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.12
21 23 0.57
22 12 0.30
ACGTcount: A:0.18, C:0.01, G:0.31, T:0.49
Consensus pattern (21 bp):
TTTTAAGGTTAGGGTTTAGAG
Found at i:1438510 original size:14 final size:14
Alignment explanation
Indices: 1438462--1438684 Score: 74
Period size: 14 Copynumber: 15.4 Consensus size: 14
1438452 CAAGCGCTTG
*
1438462 GGGTTTTGATTTTG
1 GGGTTTTGATTTTA
** *
1438476 GGGTTCGGAGGTTTA
1 GGGTTTTGA-TTTTA
*
1438491 GAGTTTTGATTTTA
1 GGGTTTTGATTTTA
* *
1438505 GGG-TTTAAGGTTTA
1 GGGTTTTGA-TTTTA
* * *
1438519 TGGTTTGGAGGATTTA
1 GGGTTTTGA--TTTTA
* *
1438535 AGGTTTAGATTTTA
1 GGGTTTTGATTTTA
* * *
1438549 AGGTTTTAATTTTG
1 GGGTTTTGATTTTA
* *
1438563 GGGTTTAGAGGTTTA
1 GGGTTTTGA-TTTTA
*
1438578 GAGTTTTGATTTTA
1 GGGTTTTGATTTTA
* ** * *
1438592 AGGTTTAAAGTTCA
1 GGGTTTTGATTTTA
1438606 GGGTTTT-AGTTTTA
1 GGGTTTTGA-TTTTA
** * *
1438620 TAGTTTAGAAGATTTA
1 GGGTTTTG-A-TTTTA
1438636 GGGTTTTGATTTTA
1 GGGTTTTGATTTTA
*
1438650 AGG-TTTGAGTTTTCA
1 GGGTTTTGA-TTTT-A
*
1438665 GGGTTTCGATTTTA
1 GGGTTTTGATTTTA
1438679 GGGTTT
1 GGGTTT
1438685 AGAGGATTTA
Statistics
Matches: 148, Mismatches: 50, Indels: 22
0.67 0.23 0.10
Matches are distributed among these distances:
13 10 0.07
14 81 0.55
15 30 0.20
16 27 0.18
ACGTcount: A:0.20, C:0.02, G:0.30, T:0.48
Consensus pattern (14 bp):
GGGTTTTGATTTTA
Found at i:1438529 original size:43 final size:42
Alignment explanation
Indices: 1438476--1438611 Score: 139
Period size: 43 Copynumber: 3.1 Consensus size: 42
1438466 TTTGATTTTG
*
1438476 GGGTTCGGAGGTTTAGAGTTTTGATTTTAGGGTTTAAGGTTTA
1 GGGTTTGGAGGTTTAGAGTTTTGATTTTAGGGTTTAA-GTTTA
* * * * *
1438519 TGGTTTGGAGGATTTA-AGGTTTAGATTTTAAGGTTTTAATTTTG
1 GGGTTTGGAGG-TTTAGA-GTTTTGATTTT-AGGGTTTAAGTTTA
* * *
1438563 GGGTTTAGAGGTTTAGAGTTTTGATTTTAAGGTTTAAAGTTCA
1 GGGTTTGGAGGTTTAGAGTTTTGATTTTAGGGTTT-AAGTTTA
1438606 GGGTTT
1 GGGTTT
1438612 TAGTTTTATA
Statistics
Matches: 74, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
42 5 0.07
43 34 0.46
44 27 0.36
45 8 0.11
ACGTcount: A:0.21, C:0.01, G:0.31, T:0.46
Consensus pattern (42 bp):
GGGTTTGGAGGTTTAGAGTTTTGATTTTAGGGTTTAAGTTTA
Found at i:1438641 original size:87 final size:86
Alignment explanation
Indices: 1438462--1438685 Score: 238
Period size: 87 Copynumber: 2.6 Consensus size: 86
1438452 CAAGCGCTTG
* * * *
1438462 GGGTTTTGATTTTGGGGTTCGGAGGTTTAGAGTTTTGATTTTAGGGTTTAAGGTTTATGGTTTGG
1 GGGTTTTGATTTTGGGGTT-TGAGGTTTAGAGTTTTGATTTTAGGGTTTAAAGTTCAGGGTTTGG
*
1438527 AGGATTTAAGGTTTAGATTTTA
65 AGGATTTAAGGTTTAGAATTTA
* * * *
1438549 AGGTTTTAATTTTGGGGTTTAGAGGTTTAGAGTTTTGATTTTAAGGTTTAAAGTTCAGGGTTT-T
1 GGGTTTTGATTTTGGGGTTT-GAGGTTTAGAGTTTTGATTTTAGGGTTTAAAGTTCAGGGTTTGG
*
1438613 A-GTTTTATA-GTTTAGAAGATTTA
65 AGGATTTA-AGGTTTAG-A-ATTTA
** * * *
1438636 GGGTTTTGATTTTAAGGTTTGAGTTTTCAGGGTTTCGATTTTAGGGTTTA
1 GGGTTTTGATTTTGGGGTTTGAGGTTT-AGAGTTTTGATTTTAGGGTTTA
1438686 GAGGATTTAG
Statistics
Matches: 114, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
85 11 0.10
86 9 0.08
87 94 0.82
ACGTcount: A:0.21, C:0.02, G:0.29, T:0.48
Consensus pattern (86 bp):
GGGTTTTGATTTTGGGGTTTGAGGTTTAGAGTTTTGATTTTAGGGTTTAAAGTTCAGGGTTTGGA
GGATTTAAGGTTTAGAATTTA
Found at i:1438655 original size:58 final size:60
Alignment explanation
Indices: 1438531--1438895 Score: 199
Period size: 58 Copynumber: 6.3 Consensus size: 60
1438521 GTTTGGAGGA
* * * * * * *
1438531 TTTAAGGTTTAGA-TTTTAAGGTTTTA-ATTTTGGGGTTTAG-AGGTTTAGAGTTTTGAT
1 TTTAAGGTTTAAAGTTTCAGGGTTTTAGATTTTAGAGTTTAGAAGATTTAGGGTTTTGAT
*
1438588 TTTAAGGTTTAAAG-TTCAGGGTTTTAG-TTTTATAGTTTAGAAGATTTAGGGTTTTGAT
1 TTTAAGGTTTAAAGTTTCAGGGTTTTAGATTTTAGAGTTTAGAAGATTTAGGGTTTTGAT
* * * * * **
1438646 TTTAAGGTTT-GAGTTTTCAGGG-TTTCGATTTTAGGGTTTAGAGGATTTAGGATTTCAAT
1 TTTAAGGTTTAAAG-TTTCAGGGTTTTAGATTTTAGAGTTTAGAAGATTTAGGGTTTTGAT
* * * * * * * * * *
1438705 TTTATGGTTT-GAGGTTCATGG-TTTCGATTTTAGGGTTTGGAGGCTTTATGGTTTTGAT
1 TTTAAGGTTTAAAGTTTCAGGGTTTTAGATTTTAGAGTTTAGAAGATTTAGGGTTTTGAT
* ** ** * * *
1438763 TTAAAGG-TTCGAGTTTTGGGGTTTTA-ATTTTA-AGATTT-GATGGCTTTAAGGTTTTGAT
1 TTTAAGGTTTAAAGTTTCAGGGTTTTAGATTTTAGAG-TTTAGA-AGATTTAGGGTTTTGAT
* * * * *
1438821 TTTAGGGTTCGAAAGATTT-AGGGTTTT-GATTTTATAGTCT--AAGGTTT-GAGGTTTTGAT
1 TTTAAGGTT-TAAAG-TTTCAGGGTTTTAGATTTTAGAGTTTAGAAGATTTAG-GGTTTTGAT
*
1438879 TTTAAGGTTTGAAGTTT
1 TTTAAGGTTTAAAGTTT
1438896 GAGGTTTAGT
Statistics
Matches: 245, Mismatches: 47, Indels: 33
0.75 0.14 0.10
Matches are distributed among these distances:
56 3 0.01
57 42 0.17
58 129 0.53
59 49 0.20
60 17 0.07
61 5 0.02
ACGTcount: A:0.22, C:0.03, G:0.27, T:0.48
Consensus pattern (60 bp):
TTTAAGGTTTAAAGTTTCAGGGTTTTAGATTTTAGAGTTTAGAAGATTTAGGGTTTTGAT
Found at i:1438741 original size:14 final size:14
Alignment explanation
Indices: 1438632--1438742 Score: 73
Period size: 14 Copynumber: 7.7 Consensus size: 14
1438622 GTTTAGAAGA
*
1438632 TTTAGGGTTTTGAT
1 TTTAGGGTTTCGAT
*
1438646 TTTAAGGTTT-GAGT
1 TTTAGGGTTTCGA-T
1438660 TTTCAGGGTTTCGAT
1 TTT-AGGGTTTCGAT
* *
1438675 TTTAGGGTTTAGAGGA
1 TTTAGGGTTTCGA--T
* *
1438691 TTTAGGATTTCAAT
1 TTTAGGGTTTCGAT
* *
1438705 TTTATGGTTT-GAGG
1 TTTAGGGTTTCGA-T
* *
1438719 TTCATGGTTTCGAT
1 TTTAGGGTTTCGAT
1438733 TTTAGGGTTT
1 TTTAGGGTTT
1438743 GGAGGCTTTA
Statistics
Matches: 74, Mismatches: 16, Indels: 14
0.71 0.15 0.13
Matches are distributed among these distances:
13 3 0.04
14 47 0.64
15 12 0.16
16 12 0.16
ACGTcount: A:0.18, C:0.05, G:0.28, T:0.50
Consensus pattern (14 bp):
TTTAGGGTTTCGAT
Found at i:1439042 original size:3 final size:3
Alignment explanation
Indices: 1439034--1439097 Score: 71
Period size: 3 Copynumber: 21.7 Consensus size: 3
1439024 TAATGAAAAT
*
1439034 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA GTT- TT- TTA TTT TTAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TT-A
*
1439079 TT- TTA TTA TTA TTA CTA TT
1 TTA TTA TTA TTA TTA TTA TT
1439098 TAATAATTCT
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 6 0.11
3 43 0.81
4 4 0.08
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1439261 original size:11 final size:12
Alignment explanation
Indices: 1439234--1439266 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1439224 TTACTCTTCA
1439234 TTATTATTCTCTT
1 TTATTATT-TCTT
1439247 TTATTATTT-TT
1 TTATTATTTCTT
1439258 TTATTATTT
1 TTATTATTT
1439267 ACCTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.55
12 1 0.05
13 8 0.40
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (12 bp):
TTATTATTTCTT
Found at i:1439429 original size:21 final size:21
Alignment explanation
Indices: 1439405--1439456 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1439395 AAACATTAAT
1439405 AATAAAATTT-AAAATAAAAAA
1 AATAAAATTTAAAAAT-AAAAA
* *
1439426 AATAATATATAAAAATAAAAA
1 AATAAAATTTAAAAATAAAAA
1439447 AATAAAATTT
1 AATAAAATTT
1439457 TTTTGGTACC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (21 bp):
AATAAAATTTAAAAATAAAAA
Found at i:1439444 original size:27 final size:26
Alignment explanation
Indices: 1439401--1439454 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
1439391 GCATAAACAT
*
1439401 TAATAATAAAATTTAAAATAAAAAAAA
1 TAATAATAAAATATAAAA-AAAAAAAA
*
1439428 TAATATATAAAA-ATAAAAAAATAAAA
1 TAATA-ATAAAATATAAAAAAAAAAAA
1439454 T
1 T
1439455 TTTTTTGGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 8 0.33
27 10 0.42
28 6 0.25
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (26 bp):
TAATAATAAAATATAAAAAAAAAAAA
Found at i:1440955 original size:34 final size:34
Alignment explanation
Indices: 1440917--1440993 Score: 91
Period size: 34 Copynumber: 2.3 Consensus size: 34
1440907 AAAAGTAACG
* ** *
1440917 AGATTGATATTGAACCGTGAGTCAAAAAATAATA
1 AGATTGATATTAAACCACGAGTCAAAAAATAAAA
* *
1440951 AGATTGAGATTAAACTACGAGTCAAAAAATAAAA
1 AGATTGATATTAAACCACGAGTCAAAAAATAAAA
*
1440985 AGATAGATA
1 AGATTGATA
1440994 AATAATGAGT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.52, C:0.08, G:0.17, T:0.23
Consensus pattern (34 bp):
AGATTGATATTAAACCACGAGTCAAAAAATAAAA
Found at i:1441004 original size:31 final size:34
Alignment explanation
Indices: 1440934--1441250 Score: 122
Period size: 34 Copynumber: 9.5 Consensus size: 34
1440924 TATTGAACCG
*
1440934 TGAGTCAAAAAATAATAAGATTGAGATTAAACTA
1 TGAGTCAAAAAATAAAAAGATTGAGATTAAACTA
*
1440968 CGAGTCAAAAAATAAAAAGA-T-AGA-TAAA-TAA
1 TGAGTCAAAAAATAAAAAGATTGAGATTAAACT-A
* * * * *
1440999 TGAGTCAGAGAATAAAAGGACTGGGATTAAAC--
1 TGAGTCAAAAAATAAAAAGATTGAGATTAAACTA
** **
1441031 TGCATGTCAAAAAATAACGAGATCAAGATTGAAAGGC-A
1 TG-A-GTCAAAAAATAAAAAGATTGAGATT-AAA--CTA
* * ** * * * *
1441069 --AGTAAAAAAATAACAAGAACGGGATTGAATTG
1 TGAGTCAAAAAATAAAAAGATTGAGATTAAACTA
1441101 TGAGTCAAAAAATAAAAAGA-T-AGATTAAA-TA
1 TGAGTCAAAAAATAAAAAGATTGAGATTAAACTA
* * * *
1441132 GTGAGTCAAAGAATAAAAAGACTGGGATTAAACCA
1 -TGAGTCAAAAAATAAAAAGATTGAGATTAAACTA
* * * ** **
1441167 -CACGTTAGAAAATAATGAGATCAAGATTGAAAC-A
1 TGA-GTCAAAAAATAAAAAGATTGAGATT-AAACTA
* * *** *
1441201 CGAGTCAAAAAATAACAAGACCAAGATTAAACTG
1 TGAGTCAAAAAATAAAAAGATTGAGATTAAACTA
*
1441235 CGAGTCAAAAAATAAA
1 TGAGTCAAAAAATAAA
1441251 GATGACTGAG
Statistics
Matches: 210, Mismatches: 51, Indels: 44
0.69 0.17 0.14
Matches are distributed among these distances:
30 1 0.00
31 22 0.10
32 31 0.15
33 12 0.06
34 133 0.63
35 10 0.05
37 1 0.00
ACGTcount: A:0.53, C:0.10, G:0.18, T:0.19
Consensus pattern (34 bp):
TGAGTCAAAAAATAAAAAGATTGAGATTAAACTA
Found at i:1441026 original size:133 final size:133
Alignment explanation
Indices: 1440867--1441250 Score: 473
Period size: 134 Copynumber: 2.9 Consensus size: 133
1440857 ATTAAACGGC
* * ** * *
1440867 GAGTTAGAGAATAAAAGGACTAGGATTAAACTGCACGTAAAAAAGTAACGAGATTGATATTGAAC
1 GAGTCAGAGAATAAAAGGACTGGGATTAAACTGCACGTAAAAAA-TAACGAGATCAAGATTGAAA
* * ** *
1440932 CGTGAGTCAAAAAATAATAAGATTGAGATTAAACTACGAGTCAAAAAATAAAAAGATAGA-TAAA
65 CGCGAGTCAAAAAATAACAAGAACGAGATTAAACTGCGAGTCAAAAAATAAAAAGATAGATTAAA
1440996 TAAT
130 TAAT
*
1441000 GAGTCAGAGAATAAAAGGACTGGGATTAAACTGCATGTCAAAAAATAACGAGATCAAGATTGAAA
1 GAGTCAGAGAATAAAAGGACTGGGATTAAACTGCACGT-AAAAAATAACGAGATCAAGATTGAAA
* * * * * * *
1441065 GGCAAGTAAAAAAATAACAAGAACGGGATTGAATTGTGAGTCAAAAAATAAAAAGATAGATTAAA
65 CGCGAGTCAAAAAATAACAAGAACGAGATTAAACTGCGAGTCAAAAAATAAAAAGATAGATTAAA
*
1441130 TAGT
130 TAAT
* * ** * *
1441134 GAGTCAAAGAATAAAAAGACTGGGATTAAACCACACGTTAGAAAATAATGAGATCAAGATTGAAA
1 GAGTCAGAGAATAAAAGGACTGGGATTAAACTGCACG-TAAAAAATAACGAGATCAAGATTGAAA
* * *
1441199 CACGAGTCAAAAAATAACAAGACCAAGATTAAACTGCGAGTCAAAAAATAAA
65 CGCGAGTCAAAAAATAACAAGAACGAGATTAAACTGCGAGTCAAAAAATAAA
1441251 GATGACTGAG
Statistics
Matches: 211, Mismatches: 37, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
133 99 0.47
134 111 0.53
135 1 0.00
ACGTcount: A:0.52, C:0.10, G:0.19, T:0.19
Consensus pattern (133 bp):
GAGTCAGAGAATAAAAGGACTGGGATTAAACTGCACGTAAAAAATAACGAGATCAAGATTGAAAC
GCGAGTCAAAAAATAACAAGAACGAGATTAAACTGCGAGTCAAAAAATAAAAAGATAGATTAAAT
AAT
Found at i:1441213 original size:34 final size:34
Alignment explanation
Indices: 1441175--1441286 Score: 104
Period size: 34 Copynumber: 3.3 Consensus size: 34
1441165 CACACGTTAG
1441175 AAAATAATGAGATCAAGATTGAAACACGAGTCAA
1 AAAATAATGAGATCAAGATTGAAACACGAGTCAA
** * *
1441209 AAAATAACAAGACCAAGATT-AAACTGCGAGTCAA
1 AAAATAATGAGATCAAGATTGAAAC-ACGAGTCAA
* * * *
1441243 AAAATAA--AGATGACTGAGTTGAATCACAAGTCAA
1 AAAATAATGAGATCA-AGA-TTGAAACACGAGTCAA
1441277 AAAATAATGA
1 AAAATAATGA
1441287 TTATTAGGAT
Statistics
Matches: 62, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
32 4 0.06
33 6 0.10
34 48 0.77
35 3 0.05
36 1 0.02
ACGTcount: A:0.54, C:0.12, G:0.16, T:0.18
Consensus pattern (34 bp):
AAAATAATGAGATCAAGATTGAAACACGAGTCAA
Found at i:1441247 original size:68 final size:67
Alignment explanation
Indices: 1441021--1441283 Score: 187
Period size: 68 Copynumber: 3.9 Consensus size: 67
1441011 TAAAAGGACT
* ** *
1441021 GGGATTAAACTGCATGTCAAAAAATAACGAGATCAAGATTGAAAGGCAAGTAAAAAAATAACAAG
1 GGGATTAAACTGCACGTCAAAAAATAA-GAGATCAAGATTGAAACACAAGTCAAAAAATAACAAG
*
1441086 AAC
65 ACC
* * * * * ** * *
1441089 GGGATTGAATTGTGA-GTCAAAAAATAAAAAGAT--AGATT-AAATAGTGAGTCAAAGAATAAAA
1 GGGATTAAACTG-CACGTCAAAAAAT-AAGAGATCAAGATTGAAACA-CAAGTCAAAAAATAACA
*
1441150 AGACT
63 AGACC
** * * *
1441155 GGGATTAAACCACACGTTAGAAAATAATGAGATCAAGATTGAAACACGAGTCAAAAAATAACAAG
1 GGGATTAAACTGCACGTCAAAAAATAA-GAGATCAAGATTGAAACACAAGTCAAAAAATAACAAG
1441220 ACC
65 ACC
** * * *
1441223 AAGATTAAACTGCGA-GTCAAAAAATAA-AGATGACTGAGTTGAATCACAAGTCAAAAAATAA
1 GGGATTAAACTGC-ACGTCAAAAAATAAGAGATCA-AGA-TTGAAACACAAGTCAAAAAATAA
1441284 TGATTATTAG
Statistics
Matches: 148, Mismatches: 36, Indels: 22
0.72 0.17 0.11
Matches are distributed among these distances:
65 6 0.04
66 45 0.30
67 2 0.01
68 87 0.59
69 8 0.05
ACGTcount: A:0.52, C:0.11, G:0.19, T:0.19
Consensus pattern (67 bp):
GGGATTAAACTGCACGTCAAAAAATAAGAGATCAAGATTGAAACACAAGTCAAAAAATAACAAGA
CC
Found at i:1441281 original size:102 final size:100
Alignment explanation
Indices: 1441102--1441286 Score: 221
Period size: 102 Copynumber: 1.8 Consensus size: 100
1441092 ATTGAATTGT
* * * *
1441102 GAGTCAAAAAATAAAAAGATAGATTAAATAGTGAGTCAAAGAATAAAAAGACTGGGATTAAACCA
1 GAGTCAAAAAATAAAAAGAAAGATTAAATAGCGAGTCAAAAAATAAAAAGACTGAGATTAAACCA
* * *
1441167 CACGTTAGAAAATAATGAGATCAAGATTGAAACAC
66 CAAGTCAAAAAATAATGAGATCAAGATTGAAACAC
* * *
1441202 GAGTCAAAAAATAACAAGACCAAGATTAAACT-GCGAGTCAAAAAATAAAGATGACTGAG-TTGA
1 GAGTCAAAAAATAAAAAGA--AAGATTAAA-TAGCGAGTCAAAAAATAAA-AAGACTGAGATTAA
*
1441265 ATCACAAGTCAAAAAATAATGA
62 ACCACAAGTCAAAAAATAATGA
1441287 TTATTAGGAT
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
100 18 0.26
102 44 0.63
103 8 0.11
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.18
Consensus pattern (100 bp):
GAGTCAAAAAATAAAAAGAAAGATTAAATAGCGAGTCAAAAAATAAAAAGACTGAGATTAAACCA
CAAGTCAAAAAATAATGAGATCAAGATTGAAACAC
Found at i:1441422 original size:34 final size:33
Alignment explanation
Indices: 1441378--1441490 Score: 93
Period size: 34 Copynumber: 3.4 Consensus size: 33
1441368 GAACTGTGAA
* * *
1441378 TCAAATAATAAAAAGACCAAGATTAAACTACAAG
1 TCAAAAAATAAAAAGA-CAAGATTAAACAACGAG
* * * **
1441412 TCAAAAAATAACAAGATCAGGATTGAACCGCGAG
1 TCAAAAAATAAAAAGA-CAAGATTAAACAACGAG
**
1441446 TCAAAAAATAACGAGACAA-ATTAAACAACGAG
1 TCAAAAAATAAAAAGACAAGATTAAACAACGAG
* *
1441478 TCGAAGAATAAAA
1 TCAAAAAATAAAA
1441491 GGATTGAGAT
Statistics
Matches: 62, Mismatches: 17, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
32 19 0.31
33 2 0.03
34 41 0.66
ACGTcount: A:0.56, C:0.15, G:0.14, T:0.15
Consensus pattern (33 bp):
TCAAAAAATAAAAAGACAAGATTAAACAACGAG
Found at i:1441605 original size:35 final size:34
Alignment explanation
Indices: 1441511--1441608 Score: 108
Period size: 34 Copynumber: 2.9 Consensus size: 34
1441501 TAAATCGCAT
* *
1441511 GTAAGAAAATAACGAGAT-TGGAATTGAACCGCAA
1 GTAAAAAAATAACGAGATCTGG-ATTGAACAGCAA
* * **
1441545 GTAAAAAAATAACAAAATCAAGATTGAACAGCAA
1 GTAAAAAAATAACGAGATCTGGATTGAACAGCAA
*
1441579 GTCAAAAAATAACGATGATCTGGATTGAAC
1 GTAAAAAAATAACGA-GATCTGGATTGAAC
1441609 CATGAGTCAA
Statistics
Matches: 51, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
34 39 0.76
35 12 0.24
ACGTcount: A:0.51, C:0.12, G:0.18, T:0.18
Consensus pattern (34 bp):
GTAAAAAAATAACGAGATCTGGATTGAACAGCAA
Done.