Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006607.1 Hibiscus syriacus cultivar Beakdansim tig00016212_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1995858
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 8
Found at i:1242829 original size:29 final size:29
Alignment explanation
Indices: 1242745--1242829 Score: 89
Period size: 29 Copynumber: 2.9 Consensus size: 29
1242735 TCCTAACTCT
* * * ***
1242745 TGTTCTTCACTCGTCAGCTTCTGTTCTGT
1 TGTTCTTGACTCCTCACCTTCTGTTCCAA
*
1242774 TGTTCTTGACTCCTCACCTTTTGTTCCAA
1 TGTTCTTGACTCCTCACCTTCTGTTCCAA
* *
1242803 TGTTCTTTACTTCTCACCTTCTGTTCC
1 TGTTCTTGACTCCTCACCTTCTGTTCC
1242830 CAACTTATCA
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.09, C:0.31, G:0.12, T:0.48
Consensus pattern (29 bp):
TGTTCTTGACTCCTCACCTTCTGTTCCAA
Found at i:1245541 original size:2 final size:2
Alignment explanation
Indices: 1245536--1245570 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1245526 AATGTGTGTG
1245536 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1245571 TATTCTCTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1245704 original size:31 final size:31
Alignment explanation
Indices: 1245666--1245727 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
1245656 AATTCAGATG
1245666 TCGACACCTACATTAATTTTCCCCTTGTTCC
1 TCGACACCTACATTAATTTTCCCCTTGTTCC
1245697 TCGACACCTACATTAATTTTCCCCTTGTTCC
1 TCGACACCTACATTAATTTTCCCCTTGTTCC
1245728 CCGTACTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.19, C:0.35, G:0.06, T:0.39
Consensus pattern (31 bp):
TCGACACCTACATTAATTTTCCCCTTGTTCC
Found at i:1253809 original size:31 final size:31
Alignment explanation
Indices: 1253771--1253832 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
1253761 ATGAAATTTC
1253771 TAGTAAATTTCATGTTAATTTACCTTATATT
1 TAGTAAATTTCATGTTAATTTACCTTATATT
1253802 TAGTAAATTTCATGTTAATTTACCTTATATT
1 TAGTAAATTTCATGTTAATTTACCTTATATT
1253833 AAGCTTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.10, G:0.06, T:0.52
Consensus pattern (31 bp):
TAGTAAATTTCATGTTAATTTACCTTATATT
Found at i:1258683 original size:13 final size:13
Alignment explanation
Indices: 1258646--1258683 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
1258636 CATGCCATGA
*
1258646 CAACCAAAATTTT
1 CAACCAATATTTT
1258659 CAACCAATTATTTT
1 CAACCAA-TATTTT
1258673 CAACCAATATT
1 CAACCAATATT
1258684 GACTAAGTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.42, C:0.24, G:0.00, T:0.34
Consensus pattern (13 bp):
CAACCAATATTTT
Found at i:1261093 original size:15 final size:14
Alignment explanation
Indices: 1261073--1261122 Score: 57
Period size: 15 Copynumber: 3.5 Consensus size: 14
1261063 CCTTTGAAAA
1261073 CATTTCTATCCCTTT
1 CATTTCTAT-CCTTT
*
1261088 CATTTCTTATCATTT
1 CATTTC-TATCCTTT
*
1261103 CATTTCT-TTCTTT
1 CATTTCTATCCTTT
1261116 CATTTCT
1 CATTTCT
1261123 TATTTCCATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
13 11 0.35
14 1 0.03
15 16 0.52
16 3 0.10
ACGTcount: A:0.14, C:0.26, G:0.00, T:0.60
Consensus pattern (14 bp):
CATTTCTATCCTTT
Found at i:1261121 original size:9 final size:9
Alignment explanation
Indices: 1261084--1261123 Score: 55
Period size: 9 Copynumber: 4.3 Consensus size: 9
1261074 ATTTCTATCC
1261084 CTTTCATTT
1 CTTTCATTT
1261093 CTTATCATTT
1 CTT-TCATTT
1261103 CATTTC-TTT
1 C-TTTCATTT
1261112 CTTTCATTT
1 CTTTCATTT
1261121 CTT
1 CTT
1261124 ATTTCCATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 4 0.14
9 13 0.46
10 9 0.32
11 2 0.07
ACGTcount: A:0.12, C:0.23, G:0.00, T:0.65
Consensus pattern (9 bp):
CTTTCATTT
Found at i:1261133 original size:13 final size:14
Alignment explanation
Indices: 1261084--1261125 Score: 68
Period size: 13 Copynumber: 3.0 Consensus size: 14
1261074 ATTTCTATCC
1261084 CTTTCATTTCTTAT
1 CTTTCATTTCTTAT
1261098 CATTTCATTTCTT-T
1 C-TTTCATTTCTTAT
1261112 CTTTCATTTCTTAT
1 CTTTCATTTCTTAT
1261126 TTCCATTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 11 0.42
14 4 0.15
15 11 0.42
ACGTcount: A:0.14, C:0.21, G:0.00, T:0.64
Consensus pattern (14 bp):
CTTTCATTTCTTAT
Found at i:1262500 original size:21 final size:21
Alignment explanation
Indices: 1262474--1262631 Score: 148
Period size: 21 Copynumber: 7.5 Consensus size: 21
1262464 TGCAAGTTCG
1262474 CGTTGCGATTTATTCCAAGTT
1 CGTTGCGATTTATTCCAAGTT
* * *
1262495 CGTTGCGA--TAGTCGAAATT
1 CGTTGCGATTTATTCCAAGTT
*
1262514 CGCATTGCGATTTATTCCAAATT
1 CG--TTGCGATTTATTCCAAGTT
*
1262537 CGTTGCGA--TAGTCCAAGTT
1 CGTTGCGATTTATTCCAAGTT
*
1262556 CGCGTTGTGATTTATTCCAAGTT
1 --CGTTGCGATTTATTCCAAGTT
* *
1262579 CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAGTT
1262598 CGCGTTGCGATTTATTCCAAGTT
1 --CGTTGCGATTTATTCCAAGTT
1262621 CGTTGCGATTT
1 CGTTGCGATTT
1262632 TCCAAAATCG
Statistics
Matches: 111, Mismatches: 14, Indels: 24
0.74 0.09 0.16
Matches are distributed among these distances:
19 28 0.25
21 53 0.48
23 30 0.27
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (21 bp):
CGTTGCGATTTATTCCAAGTT
Found at i:1262529 original size:42 final size:42
Alignment explanation
Indices: 1262467--1262629 Score: 281
Period size: 42 Copynumber: 3.9 Consensus size: 42
1262457 AAATATGTGC
1262467 AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCG
1 AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCG
* * * *
1262509 AAATTCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCC
1 AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCG
*
1262551 AAGTTCGCGTTGTGATTTATTCCAAGTTCGTTGCGATAGTCG
1 AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCG
1262593 AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGAT
1 AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGAT
1262630 TTTCCAAAAT
Statistics
Matches: 111, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 111 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (42 bp):
AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCG
Found at i:1263252 original size:6 final size:6
Alignment explanation
Indices: 1263236--1263267 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
1263226 TCTCATCTCG
1263236 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1263268 AATACGTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:1263447 original size:21 final size:21
Alignment explanation
Indices: 1263421--1263474 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
1263411 GATTTACATA
1263421 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
1263442 TTCGCATTACGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
1263463 TTCGCGTTGCGA
1 TTCGCATTGCGA
1263475 ATTTGGAAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:1268888 original size:19 final size:19
Alignment explanation
Indices: 1268861--1268899 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1268851 TACTGACTGA
* * *
1268861 TTTTCTTTTGTTTTTTTAT
1 TTTTATTTTATTTTTGTAT
1268880 TTTTATTTTATTTTTGTAT
1 TTTTATTTTATTTTTGTAT
1268899 T
1 T
1268900 ACACTATTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.10, C:0.03, G:0.05, T:0.82
Consensus pattern (19 bp):
TTTTATTTTATTTTTGTAT
Found at i:1279360 original size:13 final size:14
Alignment explanation
Indices: 1279342--1279374 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
1279332 TTTCCTGAAG
1279342 AAAAAATAATA-AT
1 AAAAAATAATATAT
1279355 AAAAAATAATATAT
1 AAAAAATAATATAT
1279369 AAAAAA
1 AAAAAA
1279375 ATAAGAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AAAAAATAATATAT
Found at i:1280940 original size:133 final size:131
Alignment explanation
Indices: 1280767--1281313 Score: 563
Period size: 131 Copynumber: 4.1 Consensus size: 131
1280757 GATATGGTTT
* *
1280767 TCCCTAAAGAGTAGTGGA-ACAGA-TCCTCTTTCTTTCATATTTGGTCTTCCTAAAGAGCACTGA
1 TCCCTAAAGAGTAGTGGAGA-AGATTCTTC-TTCTTTCATATTTGGTCTTCCTGAAGAGCACTGA
* * *
1280830 AGCAAATCAAGTTCGATTCAATCTTCCTTGAAGAGCAGCGAAGTGGGTCAAAATTTTCTCGAGTC
64 AGCAAATCAAGTTCGATTCAATCTTCCCTGAAGAGCAACGAAGTGGATCAAAA--TTCTCGAGTC
1280895 TGATC
127 TGATC
* * *
1280900 TCCCTAAAGAGTAGTGGAGAAGATTCTTCTTCTTTTATATTTGGCCTTCCTGAAGAGCAGTGAAG
1 TCCCTAAAGAGTAGTGGAGAAGATTCTTCTTCTTTCATATTTGGTCTTCCTGAAGAGCACTGAAG
* * * * *
1280965 CAAATTC-A-TTACGTTTCAATCTTCCTTGAAGAGCAACAAAGTGGATCAAAATTAT-GTGTCTG
66 CAAA-TCAAGTT-CGATTCAATCTTCCCTGAAGAGCAACGAAGTGGATCAAAATTCTCGAGTCTG
*
1281027 ATT
129 ATC
* * * * *
1281030 TCCCTTAAAAAATAGTGGAGCAGATTCTTCTTCTTTCATATTTGGTCTTCCTGAAGAGAAATGAA
1 TCCC-TAAAGAGTAGTGGAGAAGATTCTTCTTCTTTCATATTTGGTCTTCCTGAAGAGCACTGAA
* * * ** *
1281095 GCAAATCGATGTT-GATTCAATCTTCCCTGAAAAGTAGTGAAGTGGATCAAAATT-AC-ATGTCT
65 GCAAATC-AAGTTCGATTCAATCTTCCCTGAAGAGCAACGAAGTGGATCAAAATTCTCGA-GTCT
1281157 GATC
128 GATC
* * * * **
1281161 TCCCCTAAAGAGTAATGGAGCATATTCTTCTTCTTTCAGATTTGGTCTTATTGAAGAGCAAC-GA
1 T-CCCTAAAGAGTAGTGGAGAAGATTCTTCTTCTTTCATATTTGGTCTTCCTGAAGAGC-ACTGA
** * * * *
1281225 ATAAAATCAAGTTTGATTCAATATTCCCTGAAGAGCAACGAAGTAGATCAAAGGTTTCTCGAGTC
64 AGCAAATCAAGTTCGATTCAATCTTCCCTGAAGAGCAACGAAGTGGATCAAA--ATTCTCGAGTC
*
1281290 TGACC
127 TGATC
1281295 TCCCCTAAAGAGTAGTGGA
1 T-CCCTAAAGAGTAGTGGA
1281314 ACATATCCCC
Statistics
Matches: 345, Mismatches: 52, Indels: 33
0.80 0.12 0.08
Matches are distributed among these distances:
130 18 0.05
131 189 0.55
132 6 0.02
133 98 0.28
134 33 0.10
135 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (131 bp):
TCCCTAAAGAGTAGTGGAGAAGATTCTTCTTCTTTCATATTTGGTCTTCCTGAAGAGCACTGAAG
CAAATCAAGTTCGATTCAATCTTCCCTGAAGAGCAACGAAGTGGATCAAAATTCTCGAGTCTGAT
C
Found at i:1281393 original size:134 final size:134
Alignment explanation
Indices: 1281153--1281395 Score: 307
Period size: 135 Copynumber: 1.8 Consensus size: 134
1281143 AAAATTACAT
* * ** * *
1281153 GTCTGATCTCCCCTAAAGAGTAATGGAGCATATTCTTCTTCTTTCAGATTTGGTCTTATTGAAGA
1 GTCTGACCTCCCCTAAAGAGTAATGGAACATATTCCCCTTCTTTCAGATTTGATCTTATTAAAGA
* *
1281218 GCAACGAATAAAATCAAGTTTGATTCAATATTCCCTGAAGAGCAACGAAGTAGATCAAAGGTTTC
66 ACAACAAATAAAATCAAGTTTGATTCAATATTCCCTGAAGAGCAACGAAGTAGATCAAAGGTTTC
1281283 TCGA
131 TCGA
* *
1281287 GTCTGACCTCCCCTAAAGAGTAGTGGAACATA-TCCCCATT-TTTCCTAGATTTGATCTTCTTAA
1 GTCTGACCTCCCCTAAAGAGTAATGGAACATATTCCCC-TTCTTT-C-AGATTTGATCTTATTAA
*
1281350 AGAACAACAAAGT-AAATCAAGTTTGGTTCAACT-TTCCCT-AAGAGCA
63 AGAACAACAAA-TAAAATCAAGTTTGATTCAA-TATTCCCTGAAGAGCA
1281396 GCAAAGTGAA
Statistics
Matches: 93, Mismatches: 11, Indels: 10
0.82 0.10 0.09
Matches are distributed among these distances:
133 6 0.06
134 39 0.42
135 46 0.49
136 2 0.02
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (134 bp):
GTCTGACCTCCCCTAAAGAGTAATGGAACATATTCCCCTTCTTTCAGATTTGATCTTATTAAAGA
ACAACAAATAAAATCAAGTTTGATTCAATATTCCCTGAAGAGCAACGAAGTAGATCAAAGGTTTC
TCGA
Found at i:1281646 original size:3 final size:3
Alignment explanation
Indices: 1281638--1281692 Score: 58
Period size: 3 Copynumber: 17.3 Consensus size: 3
1281628 TAAATATATA
*
1281638 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T AAT TAT ATAGGT TAAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TA--T T-AT TAT
1281686 TAT TAT T
1 TAT TAT T
1281693 GGTCACACGT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
2 1 0.02
3 37 0.82
4 4 0.09
5 1 0.02
6 2 0.04
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1288348 original size:17 final size:17
Alignment explanation
Indices: 1288326--1288373 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
1288316 TATTTGGTAG
1288326 TTGGGTACCAATTAAAT
1 TTGGGTACCAATTAAAT
* *
1288343 TTGGGTACCCATAAAAT
1 TTGGGTACCAATTAAAT
1288360 TTGGGTACCCAATT
1 TTGGGTA-CCAATT
1288374 CTTATATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 22 0.85
18 4 0.15
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (17 bp):
TTGGGTACCAATTAAAT
Found at i:1288503 original size:21 final size:21
Alignment explanation
Indices: 1288477--1288518 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1288467 AAAAATTAGT
1288477 GATTTAAAGTTAGTTTTAAGG
1 GATTTAAAGTTAGTTTTAAGG
*
1288498 GATTTAAATTTAGTTTTAAGG
1 GATTTAAAGTTAGTTTTAAGG
1288519 TAAAAGTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.45
Consensus pattern (21 bp):
GATTTAAAGTTAGTTTTAAGG
Found at i:1288767 original size:2 final size:2
Alignment explanation
Indices: 1288760--1288808 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1288750 TTTTAAACTA
1288760 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1288802 AT AT AT A
1 AT AT AT A
1288809 AATTATCAGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1289346 original size:2 final size:2
Alignment explanation
Indices: 1289339--1289367 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1289329 TATATTTTAA
1289339 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1289368 TTAGCCATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1290587 original size:23 final size:23
Alignment explanation
Indices: 1290530--1290578 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
1290520 TTTTGGCGTA
*
1290530 TTTT-TTTATCTTTGTGACATGT
1 TTTTCTTTGTCTTTGTGACATGT
*
1290552 TTTTCTTTGTCTTTGTGGCATGT
1 TTTTCTTTGTCTTTGTGACATGT
1290575 TTTT
1 TTTT
1290579 TGTCTTCTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.08, C:0.10, G:0.16, T:0.65
Consensus pattern (23 bp):
TTTTCTTTGTCTTTGTGACATGT
Found at i:1293501 original size:29 final size:29
Alignment explanation
Indices: 1293348--1293507 Score: 80
Period size: 29 Copynumber: 5.4 Consensus size: 29
1293338 TACATCATAT
*
1293348 GTCCCCAAACTATGACCCTCATTT-TAAATTA
1 GTCCCTAAACTATGA--CTC-TTTCTAAATTA
* * * *
1293379 GTCCCTAAACGTTTGAAT-GTTCTAACTTCA
1 GTCCCTAAAC-TATGACTCTTTCTAAATT-A
1293409 -T-CCTCAAACTATGACTCATGTTCTAAATTA
1 GTCCCT-AAACTATGACTC-T-TTCTAAATTA
* * * * * *
1293439 GGCCTTAAACTTATGAAT-ATTATAATTTCA
1 GTCCCTAAAC-TATGACTCTTTCTAAATT-A
1293469 -TCCCTAAACTATGACTCTTTCTAAATTA
1 GTCCCTAAACTATGACTCTTTCTAAATTA
*
1293497 GTCCCCAAACT
1 GTCCCTAAACT
1293508 TTTAAATATT
Statistics
Matches: 94, Mismatches: 22, Indels: 28
0.65 0.15 0.19
Matches are distributed among these distances:
28 17 0.18
29 40 0.43
30 4 0.04
31 21 0.22
32 12 0.13
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.36
Consensus pattern (29 bp):
GTCCCTAAACTATGACTCTTTCTAAATTA
Found at i:1293524 original size:58 final size:59
Alignment explanation
Indices: 1293349--1293530 Score: 199
Period size: 60 Copynumber: 3.1 Consensus size: 59
1293339 ACATCATATG
* * * *
1293349 TCCCCAAACTATGACCCTCATTT-TAAATTAGTCCCTAAACGTTTGAATGTTCTAACTTCA
1 TCCCTAAACTATGA--CTCATTTCTAAATTAGTCCCTAAACTTTTGAATATTCTAATTTCA
* * * *
1293409 T-CCTCAAACTATGACTCATGTTCTAAATTAGGCCTTAAACTTATGAATATTATAATTTCA
1 TCCCT-AAACTATGACTCAT-TTCTAAATTAGTCCCTAAACTTTTGAATATTCTAATTTCA
* * * *
1293469 TCCCTAAACTATGACTC-TTTCTAAATTAGTCCCCAAACTTTTAAATATTCCAATTTTA
1 TCCCTAAACTATGACTCATTTCTAAATTAGTCCCTAAACTTTTGAATATTCTAATTTCA
1293527 TCCC
1 TCCC
1293531 CAAATTCATC
Statistics
Matches: 102, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
58 41 0.40
59 5 0.05
60 53 0.52
61 3 0.03
ACGTcount: A:0.32, C:0.24, G:0.07, T:0.37
Consensus pattern (59 bp):
TCCCTAAACTATGACTCATTTCTAAATTAGTCCCTAAACTTTTGAATATTCTAATTTCA
Found at i:1293821 original size:60 final size:59
Alignment explanation
Indices: 1293668--1293826 Score: 144
Period size: 60 Copynumber: 2.7 Consensus size: 59
1293658 GTTTGAGATA
* * * * *
1293668 AAATTAGAATGTTTAAAAAGTTTAGGGACCAA-TTAAAATAAAAGTCATTGTTTAGGGAT
1 AAATTAAAATATTT-AAAAGTTTAAGGACCAATTTAAAATAAAAGTCATAGTTTAAGGAT
* * * ** * *
1293727 AAATTTGAAATATTCAAAAGTTTGAA-AATTAATTTAGAATCATAA-TCATAGTTTAAGGAT
1 AAA-TTAAAATATTTAAAAGTTT-AAGGACCAATTTAAAAT-AAAAGTCATAGTTTAAGGAT
1293787 GAAATTAAAATATTTAAAAGTTTAAGGACCAATTTAAAAT
1 -AAATTAAAATATTTAAAAGTTTAAGGACCAATTTAAAAT
1293827 GAGATTCATA
Statistics
Matches: 76, Mismatches: 18, Indels: 11
0.72 0.17 0.10
Matches are distributed among these distances:
59 16 0.21
60 54 0.71
61 6 0.08
ACGTcount: A:0.47, C:0.05, G:0.14, T:0.34
Consensus pattern (59 bp):
AAATTAAAATATTTAAAAGTTTAAGGACCAATTTAAAATAAAAGTCATAGTTTAAGGAT
Found at i:1298106 original size:19 final size:19
Alignment explanation
Indices: 1298074--1298125 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
1298064 TTTTATAATG
* *
1298074 TTAAATATATTATTTAATTA
1 TTAAAAATA-TATTAAATTA
1298094 TTAAAAATATATTAAATTA
1 TTAAAAATATATTAAATTA
1298113 TTATAAAA-ATATT
1 TTA-AAAATATATT
1298126 CTATTTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTAAAAATATATTAAATTA
Found at i:1298145 original size:44 final size:44
Alignment explanation
Indices: 1298086--1298169 Score: 123
Period size: 44 Copynumber: 1.9 Consensus size: 44
1298076 AAATATATTA
* * *
1298086 TTTAATTATTAAAAATATATTAAATTATTATAAAAATATTCTAT
1 TTTAATAATTAAAAATATAATAAATGATTATAAAAATATTCTAT
* *
1298130 TTTAATAATTTAAAATATAATAAATGATTATAAATATATT
1 TTTAATAATTAAAAATATAATAAATGATTATAAAAATATT
1298170 ATTATAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (44 bp):
TTTAATAATTAAAAATATAATAAATGATTATAAAAATATTCTAT
Found at i:1301821 original size:212 final size:212
Alignment explanation
Indices: 1301454--1301886 Score: 704
Period size: 212 Copynumber: 2.0 Consensus size: 212
1301444 ACTGCCTGCA
* * *
1301454 TTAACAAGTTAGCATACCCTTTTAACCCTACATATGGAGTTTTCTTCTAACACAAACTAGATATG
1 TTAACAAGTTAACATACCCTCTTAACCCTACATATGGAGGTTTCTTCTAACACAAACTAGATATG
* * * *
1301519 CAACTCATTAGGACATATGTGTGCCTGTGCTCCAATTGACTACAAGAAGCAGAAAATTTCAAGTT
66 CAACTCATTAGGACATATGTGTGCCTGTGCTCCAAATGACTACAACAAGCACAAAATCTCAAGTT
*
1301584 CAAAACTCGGGAATTCGAGTACGACTCTTAAAAGAAAAAGAAAAGCATATTTATCCATGAAATCA
131 CAAAACTCGGAAATTCGAGTACGACTCTTAAAAGAAAAAGAAAAGCATATTTATCCATGAAATCA
1301649 CCTTGACGGATGGACTT
196 CCTTGACGGATGGACTT
* *
1301666 TTAACAAGTTAACATCCCCTCTTAACCCTACATATGGAGGTTTCTTCTAACACATACTAGATATG
1 TTAACAAGTTAACATACCCTCTTAACCCTACATATGGAGGTTTCTTCTAACACAAACTAGATATG
* * * *
1301731 CAACTCATTAGTACATATGTGTGCTTGTGCTCCAAATGACTATAACAAGTACAAAATCTCAAGTT
66 CAACTCATTAGGACATATGTGTGCCTGTGCTCCAAATGACTACAACAAGCACAAAATCTCAAGTT
* * *
1301796 CGAACCTCGGAAATTCGAGTACGACTCTTAAAAGAAGAAGAAAAGCATATTTATCCATGAAATCA
131 CAAAACTCGGAAATTCGAGTACGACTCTTAAAAGAAAAAGAAAAGCATATTTATCCATGAAATCA
*
1301861 CCTTGACGGATGGCCTT
196 CCTTGACGGATGGACTT
1301878 TTAACAAGT
1 TTAACAAGT
1301887 ATCTTCATGA
Statistics
Matches: 203, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
212 203 1.00
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (212 bp):
TTAACAAGTTAACATACCCTCTTAACCCTACATATGGAGGTTTCTTCTAACACAAACTAGATATG
CAACTCATTAGGACATATGTGTGCCTGTGCTCCAAATGACTACAACAAGCACAAAATCTCAAGTT
CAAAACTCGGAAATTCGAGTACGACTCTTAAAAGAAAAAGAAAAGCATATTTATCCATGAAATCA
CCTTGACGGATGGACTT
Found at i:1306133 original size:15 final size:15
Alignment explanation
Indices: 1306098--1306132 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1306088 TTTGTACATA
1306098 TTAAAATCAAATTAT
1 TTAAAATCAAATTAT
*
1306113 TTAAAATTAAATT-T
1 TTAAAATCAAATTAT
1306127 TTAAAA
1 TTAAAA
1306133 AACTTAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
TTAAAATCAAATTAT
Found at i:1308063 original size:117 final size:117
Alignment explanation
Indices: 1307856--1308502 Score: 496
Period size: 108 Copynumber: 5.7 Consensus size: 117
1307846 AAAAAATATA
* ** *
1307856 GACGATAACATAACCAATTAATTACTGGAAACATTATCAAGCACAATAACATATTAGGTAGCGCT
1 GACGATAACATAATCGGTTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCT
* *
1307921 TATATAACATAATAGGTAGCGCCTTTTTAAAGCTGATGGGGCTTTGGAAATCT
66 TATATAACGTAATAGGTAGCGCCTTTTT-AAGCTGATGGGGCTTTGGAAATCC
*
1307974 GACGATAACATAATCGGTTAATTACT-GAAACATTATCAAGCATAGTAACATATTAGGTAGCGCT
1 GACGATAACATAATCGGTTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCT
*
1308038 TATATAACGTAATAGGTAGCGCCTTTTTAAGCTGATGGGGCTTTGAAAATCC
66 TATATAACGTAATAGGTAGCGCCTTTTTAAGCTGATGGGGCTTTGGAAATCC
* * * ** * *** * * * *
1308090 AAAGATAACAAAATATGTTAATTACT-TAATTTGTTAT-TAGTATTATCAACATATTAGGTAACG
1 GACGATAACATAATCGGTTAATTACTGGAA-ACATTATCAAGCATAAT-AACATATTAGGTAGCG
* ** ** * * * *
1308153 CTTA-A-AATGT--TA-CCAAAG----TTTAAGCAT-ATAGAGCCTTAGAAATCC
64 CTTATATAACGTAATAGGTAGCGCCTTTTTAAGC-TGATGGGGCTTTGGAAATCC
* * * *
1308198 GACGATAACATAACCGGTTAATTACTGGAAACATTACCAAGCATAATAACATATTCGGTACCGCT
1 GACGATAACATAATCGGTTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCT
* * *
1308263 TATATAGCTTAATAGGTAGCGCCTTTTTAAAGCTGATGGGGCTTTGGAAATCT
66 TATATAACGTAATAGGTAGCGCCTTTTT-AAGCTGATGGGGCTTTGGAAATCC
* * * *** ** * * *
1308316 GACGATAACAAAATAGGTTAATTACT-TAATTTGTTAT-TTGTATTATCAACATATTAGGTAACG
1 GACGATAACATAATCGGTTAATTACTGGAA-ACATTATCAAGCATAAT-AACATATTAGGTAGCG
* * ** ** * * * *
1308379 CCTA-A-AATGT--TA-CCAAAG----TTTAAGCTGATAGAGCCTTAGAAATCC
64 CTTATATAACGTAATAGGTAGCGCCTTTTTAAGCTGATGGGGCTTTGGAAATCC
* * * *
1308424 GACGATAACATAACCAGTTAATTATTGGAAACATTATCAAGCATAATAACATATTAGGTAGCACT
1 GACGATAACATAATCGGTTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCT
*
1308489 TATGTAACGTAATA
66 TATATAACGTAATA
1308503 TGTCTACCTA
Statistics
Matches: 400, Mismatches: 105, Indels: 54
0.72 0.19 0.10
Matches are distributed among these distances:
108 122 0.31
109 20 0.05
110 6 0.01
112 6 0.01
113 6 0.01
114 2 0.00
115 4 0.01
116 53 0.13
117 98 0.25
118 83 0.21
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.31
Consensus pattern (117 bp):
GACGATAACATAATCGGTTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCT
TATATAACGTAATAGGTAGCGCCTTTTTAAGCTGATGGGGCTTTGGAAATCC
Found at i:1308366 original size:226 final size:226
Alignment explanation
Indices: 1307967--1308683 Score: 965
Period size: 226 Copynumber: 3.1 Consensus size: 226
1307957 TGGGGCTTTG
* * *
1307967 GAAATCTGACGATAACATAATCGGTTAATTACT-GAAACATTATCAAGCATAGTAACATATTAGG
1 GAAATCCGACGATAACATAACCGGTTAATTACTGGAAACATTATCAAGCATAATAACATATTAGG
* * * * * *
1308031 TAGCGCTTATATAACGTAATAGGTAGCGCCTTTTT-AAGCTGATGGGGCTTTGAAAATCCAAAGA
66 TACCGCTTATATAGCTTAATAGGTAGCGCCTTTTTAAAGCTGATGGGGCTTTGGAAATCCGACGA
* *
1308095 TAACAAAATATGTTAATTACTTAATTTGTTATTAGTATTATCAACATATTAGGTAACGCTTAAAA
131 TAACAAAATAGGTTAATTACTTAATTTGTTATTAGTATTATCAACATATTAGGTAACGCCTAAAA
1308160 TGTTACCAAAGTTTAAGCAT-ATAGAGCCTTA
196 TGTTACCAAAGTTTAAGC-TGATAGAGCCTTA
* *
1308191 GAAATCCGACGATAACATAACCGGTTAATTACTGGAAACATTACCAAGCATAATAACATATTCGG
1 GAAATCCGACGATAACATAACCGGTTAATTACTGGAAACATTATCAAGCATAATAACATATTAGG
*
1308256 TACCGCTTATATAGCTTAATAGGTAGCGCCTTTTTAAAGCTGATGGGGCTTTGGAAATCTGACGA
66 TACCGCTTATATAGCTTAATAGGTAGCGCCTTTTTAAAGCTGATGGGGCTTTGGAAATCCGACGA
*
1308321 TAACAAAATAGGTTAATTACTTAATTTGTTATTTGTATTATCAACATATTAGGTAACGCCTAAAA
131 TAACAAAATAGGTTAATTACTTAATTTGTTATTAGTATTATCAACATATTAGGTAACGCCTAAAA
1308386 TGTTACCAAAGTTTAAGCTGATAGAGCCTTA
196 TGTTACCAAAGTTTAAGCTGATAGAGCCTTA
* *
1308417 GAAATCCGACGATAACATAACCAGTTAATTATTGGAAACATTATCAAGCATAATAACATATTAGG
1 GAAATCCGACGATAACATAACCGGTTAATTACTGGAAACATTATCAAGCATAATAACATATTAGG
** * * * * *
1308482 TAGCACTTATGTAACGTAATATGTCTACCTAATATGTTGCGCATTATTAAAGCTGATGGGGCCTT
66 TA-C-C-GCT-T-A--T-ATA-G-CT---TAATAGGTAGCGCCTTTTTAAAGCTGATGGGGCTTT
* * * *
1308547 AGAAATCCGACGATAACAAAATAGTTTAATTACTTAATTTGTTATCAGTGTTATCAACATATTAG
118 GGAAATCCGACGATAACAAAATAGGTTAATTACTTAATTTGTTATTAGTATTATCAACATATTAG
* * * *
1308612 GTAACGCCT-AAATGTTAACAAAATTTAAGCTGATGGAGCGTTA
183 GTAACGCCTAAAATGTTACCAAAGTTTAAGCTGATAGAGCCTTA
* **
1308655 GGAATCCGACGATAACATAATTGGTTAAT
1 GAAATCCGACGATAACATAACCGGTTAAT
1308684 CACTTGATTT
Statistics
Matches: 437, Mismatches: 40, Indels: 18
0.88 0.08 0.04
Matches are distributed among these distances:
224 31 0.07
225 61 0.14
226 179 0.41
227 1 0.00
228 1 0.00
229 1 0.00
230 1 0.00
231 1 0.00
233 1 0.00
234 3 0.01
235 1 0.00
236 2 0.00
238 55 0.13
239 99 0.23
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.32
Consensus pattern (226 bp):
GAAATCCGACGATAACATAACCGGTTAATTACTGGAAACATTATCAAGCATAATAACATATTAGG
TACCGCTTATATAGCTTAATAGGTAGCGCCTTTTTAAAGCTGATGGGGCTTTGGAAATCCGACGA
TAACAAAATAGGTTAATTACTTAATTTGTTATTAGTATTATCAACATATTAGGTAACGCCTAAAA
TGTTACCAAAGTTTAAGCTGATAGAGCCTTA
Found at i:1308845 original size:2 final size:2
Alignment explanation
Indices: 1308840--1308864 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1308830 TATATATATA
1308840 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
1308865 CGATTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1312640 original size:18 final size:18
Alignment explanation
Indices: 1312619--1312664 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
1312609 GAATCCCTTT
*
1312619 GTTGAGAAGAAGAGTT-TG
1 GTTGAGAAGAAG-GTTGTC
1312637 GTTGAGAAGAAGGTTGTC
1 GTTGAGAAGAAGGTTGTC
1312655 GTTGAGAAGA
1 GTTGAGAAGA
1312665 CCTGCACCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 3 0.12
18 23 0.88
ACGTcount: A:0.33, C:0.02, G:0.39, T:0.26
Consensus pattern (18 bp):
GTTGAGAAGAAGGTTGTC
Found at i:1313021 original size:12 final size:12
Alignment explanation
Indices: 1313004--1313056 Score: 69
Period size: 12 Copynumber: 4.8 Consensus size: 12
1312994 TATCATTTTA
1313004 TATAATTAAATT
1 TATAATTAAATT
1313016 TATAATTAAATT
1 TATAATTAAATT
*
1313028 TATCA-T---TT
1 TATAATTAAATT
1313036 TATAATTAAATT
1 TATAATTAAATT
1313048 TATAATTAA
1 TATAATTAA
1313057 TTATTTTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
8 6 0.17
9 1 0.03
11 1 0.03
12 27 0.77
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (12 bp):
TATAATTAAATT
Found at i:1313040 original size:32 final size:34
Alignment explanation
Indices: 1312991--1313056 Score: 118
Period size: 32 Copynumber: 2.0 Consensus size: 34
1312981 ATTTACCTGT
1312991 ATTTATCATTTTATATAATTAAATTTATAATTAA
1 ATTTATCATTTTATATAATTAAATTTATAATTAA
1313025 ATTTATCA-TTT-TATAATTAAATTTATAATTAA
1 ATTTATCATTTTATATAATTAAATTTATAATTAA
1313057 TTATTTTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 21 0.66
33 3 0.09
34 8 0.25
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (34 bp):
ATTTATCATTTTATATAATTAAATTTATAATTAA
Found at i:1315572 original size:196 final size:194
Alignment explanation
Indices: 1315054--1315773 Score: 1061
Period size: 194 Copynumber: 3.7 Consensus size: 194
1315044 TTTTCTTTTA
* * * *
1315054 AAAGTATTGATAATATCTTACATATACTTATTGAAGTATCGATACCTTCAACATATCCGGTAGCT
1 AAAGTATCGATAATATATTACATATACTTATTAAAGTATCGATACCTTCAACATATCCGGTAGAT
* * * * *
1315119 TTTTACCGGTTTTATCATACTGAAACAGGTTTTGTTATATTTTTACCTGC-TATATTGTTATGTA
66 ATTTACCGGTTTTGTCATAATGAAACCGGTTTTGTCATATTTTTACCT-CTTATATTGTTATGTA
*
1315183 TCGATACATGTTTATAAAGTATCGATACTTTATAGGCGCTATTATTGCAATTCATTTAAATTCCT
130 TCGATACATGTTTATAAAGTATCGATACTTTATAGGCGCTATTATTGCAATTCTTTTAAATTCCT
* * * *
1315248 AAAGTATCGATAATATCTTACATATACTTATTAAAGTATCGATACATTCAACATATCTGGTATAT
1 AAAGTATCGATAATATATTACATATACTTATTAAAGTATCGATACCTTCAACATATCCGGTAGAT
** *
1315313 ATTTACCGGTTTTGTCATAATGAAACCATTTTTGTCATATTTTTACCTCTTATATTATTATGTAT
66 ATTTACCGGTTTTGTCATAATGAAACCGGTTTTGTCATATTTTTACCTCTTATATTGTTATGTAT
* *
1315378 CGATACATGTTTATAAGGTATCGATACTTTATAGGCGCTGTTATTGCAATTCTTTTAAATTCCT
131 CGATACATGTTTATAAAGTATCGATACTTTATAGGCGCTATTATTGCAATTCTTTTAAATTCCT
*
1315442 AAAGTATCGATAATATGATCTATATATACTTATTAAAGTATCGATACCTTCAACATATCCGGTAG
1 AAAGTATCGATAATAT-AT-TACATATACTTATTAAAGTATCGATACCTTCAACATATCCGGTAG
** *
1315507 ATATTTACTAGTTTTGTCATAATAAAACCGGTTTTGTCATATTTTTACCTCTTATATTGTTATGT
64 ATATTTACCGGTTTTGTCATAATGAAACCGGTTTTGTCATATTTTTACCTCTTATATTGTTATGT
*
1315572 ATCGATACATGTTTATAAAGTATCGATACTTTATAGGCGCTATTATTGCAATTCTTTTAAATTTC
129 ATCGATACATGTTTATAAAGTATCGATACTTTATAGGCGCTATTATTGCAATTCTTTTAAATTCC
1315637 T
194 T
* *
1315638 AAAGTATCGATACTATGA-TACTTATACTTATTACAA-TATCGATACCTTCAACATATCCGGTAG
1 AAAGTATCGATAATAT-ATTACATATACTTATTA-AAGTATCGATACCTTCAACATATCCGGTAG
*** * * **
1315701 CGCTTTACCGGTTTTGTCATATTG-AACCTGGTGTTGTCATATTTTTACCTAATATATTGTTATG
64 ATATTTACCGGTTTTGTCATAATGAAACC-GGTTTTGTCATATTTTTACCTCTTATATTGTTATG
1315765 TATCGATAC
128 TATCGATAC
1315774 TTATTTGAAT
Statistics
Matches: 477, Mismatches: 44, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
193 5 0.01
194 289 0.61
195 3 0.01
196 180 0.38
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (194 bp):
AAAGTATCGATAATATATTACATATACTTATTAAAGTATCGATACCTTCAACATATCCGGTAGAT
ATTTACCGGTTTTGTCATAATGAAACCGGTTTTGTCATATTTTTACCTCTTATATTGTTATGTAT
CGATACATGTTTATAAAGTATCGATACTTTATAGGCGCTATTATTGCAATTCTTTTAAATTCCT
Found at i:1317426 original size:14 final size:15
Alignment explanation
Indices: 1317402--1317434 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1317392 TTAAATATAT
*
1317402 AAACAAGTAAAATTA
1 AAACAAGTAAAAATA
1317417 AAACAA-TAAAAATA
1 AAACAAGTAAAAATA
1317431 AAAC
1 AAAC
1317435 TAGAACGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.73, C:0.09, G:0.03, T:0.15
Consensus pattern (15 bp):
AAACAAGTAAAAATA
Found at i:1318758 original size:2 final size:2
Alignment explanation
Indices: 1318751--1318775 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1318741 GTAATTATTA
1318751 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1318776 ATAATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1318781 original size:3 final size:3
Alignment explanation
Indices: 1318773--1318851 Score: 113
Period size: 3 Copynumber: 26.3 Consensus size: 3
1318763 ATATATATAT
* * *
1318773 ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA TTT ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
1318821 CTA ATA ATA ATG ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1318852 ATAAATCAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1319178 original size:84 final size:82
Alignment explanation
Indices: 1319025--1319208 Score: 217
Period size: 84 Copynumber: 2.2 Consensus size: 82
1319015 TCAGATGAAT
* * * * * *
1319025 TCTTCTCATTATGAACTTTCTGCTGGGGATGATGTTGACCTATTTTCTTCTGTGATAGAGTCATT
1 TCTTCTCATTATGAACTTTCTGCTGGGGATGATGCTAACCTATCTACTTCTGTGATAGAATCATG
*
1319090 CAAAAGATTAAATAAGC
66 CAAAAGATTAAACAAGC
* * *
1319107 TCTTCTCATTATGAACTTTCT-CTGGAAAGGTTGATGCTAATCTATCTACTTCTGTGATAGAATT
1 TCTTCTCATTATGAACTTTCTGCTGG---GGATGATGCTAACCTATCTACTTCTGTGATAGAATC
* *
1319171 ATGCAAAAGGTTGAACAAGC
63 ATGCAAAAGATTAAACAAGC
*
1319191 TCTTCTCATTGTGAACTT
1 TCTTCTCATTATGAACTT
1319209 CTTCTTCTTC
Statistics
Matches: 86, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
81 4 0.05
82 21 0.24
84 61 0.71
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (82 bp):
TCTTCTCATTATGAACTTTCTGCTGGGGATGATGCTAACCTATCTACTTCTGTGATAGAATCATG
CAAAAGATTAAACAAGC
Found at i:1319231 original size:36 final size:36
Alignment explanation
Indices: 1319191--1319279 Score: 151
Period size: 36 Copynumber: 2.5 Consensus size: 36
1319181 TTGAACAAGC
*
1319191 TCTTCTCATTGTGAACTTCTTCTTCTTCAGATGAGT
1 TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
*
1319227 TCTTCTCATTATGAACTTCTTTTTCTTCAGATGAGT
1 TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
*
1319263 TTTTCTCATTATGAACT
1 TCTTCTCATTATGAACT
1319280 CTACCTGGCA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.19, C:0.20, G:0.11, T:0.49
Consensus pattern (36 bp):
TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
Found at i:1319412 original size:38 final size:39
Alignment explanation
Indices: 1319333--1319435 Score: 127
Period size: 38 Copynumber: 2.6 Consensus size: 39
1319323 AGGTTGAACA
*
1319333 AATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGACG
1 AATTCTTCTAATTATGAAC----TCTTCCTTCTTCAGATGACG
*
1319376 AATTCTTCTAATTATGAACTCTT-CTTCTTCATATGACG
1 AATTCTTCTAATTATGAACTCTTCCTTCTTCAGATGACG
* *
1319414 AGTTCTTCTGATTATGAACTCT
1 AATTCTTCTAATTATGAACTCT
1319436 ATCTGGCAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
38 34 0.61
39 4 0.07
43 18 0.32
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.45
Consensus pattern (39 bp):
AATTCTTCTAATTATGAACTCTTCCTTCTTCAGATGACG
Found at i:1319456 original size:154 final size:147
Alignment explanation
Indices: 1319174--1319548 Score: 517
Period size: 154 Copynumber: 2.5 Consensus size: 147
1319164 TAGAATTATG
** * *
1319174 CAAAAGGTTGAACAAGCTCTTCTCATTGTGAAC--TTCTTCTTCTTCAGATGAGTTCTTCTCATT
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTCTTCTTCTTCAGATGAGTTCTTCTAATT
* * *
1319237 ATGAACTTCTTTTTCTTCAGATGAGTTTTTCTCATTATGAACTCTACCTGGCAATGTTAATCCAT
66 ATGAACTTCTTCTTCTTCAGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTAATCCAT
1319302 CAAATGATGAATTTAAA
131 CAAATGATGAATTTAAA
1319319 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGACGAATTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTT-TTCTT-CTTCTTCAGATGA-G--TTCTTC
* *
1319384 TAATTATGAAC-TCTTCTTCTTCATATGACGAGTTCTTCTGATTATGAACTCTATCTGGCAATGT
61 TAATTATGAACTTCTTCTTCTTC--A-GACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGT
*
1319448 TAATCCATCAATTGATGAATTTAAA
123 TAATCCATCAAATGATGAATTTAAA
* * *
1319473 CAAAAGGTTGAACAAATTCTTCTCATTATGAAC--TTCTTTTTCTTCAGATGAGTTCTTTTCATT
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTCTTCTTCTTCAGATGAGTTCTTCTAATT
*
1319536 ATGAACTTTTTCT
66 ATGAACTTCTTCT
1319549 GGAAAGGCTG
Statistics
Matches: 205, Mismatches: 14, Indels: 19
0.86 0.06 0.08
Matches are distributed among these distances:
145 30 0.15
147 15 0.07
148 10 0.05
149 14 0.07
150 13 0.06
151 15 0.07
152 16 0.08
153 1 0.00
154 91 0.44
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (147 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTCTTCTTCTTCAGATGAGTTCTTCTAATT
ATGAACTTCTTCTTCTTCAGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTAATCCAT
CAAATGATGAATTTAAA
Found at i:1319678 original size:222 final size:223
Alignment explanation
Indices: 1319378--1319790 Score: 591
Period size: 222 Copynumber: 1.9 Consensus size: 223
1319368 AGATGACGAA
* *
1319378 TTCTTCTAATTATGAACTCTTCTTCTTCATATGACGAGTTCTTCTGATTATGAACTCTATCTGGC
1 TTCTTCTAATTATGAACTCTTCTTCTTCATATGACGAGTTCTTCTCATTATGAACTCTATCTGGA
* * * *
1319443 AATGTTAATCCATCAATTGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
66 AAAGCTAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
* *
1319508 C-T-TT-TTCTTCAGATGAGTTCTTTTCATTATGAACTTTTTCTGGAAAGGCTGATCCATCAATT
131 CTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGCTGATCCATCAATT
1319570 GATGAATTCAGGCAAAAGGTTGAACAAG
196 GATGAATTCAGGCAAAAGGTTGAACAAG
* * * * *
1319598 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA-GATGAGTTCTTCTCATTATGAACTTTCTCT
1 TTCTTCTAATTATGAAC-TCTTCTT-CTTCAT-ATGACGAGTTCTTCTCATTATGAACTCTATCT
* ** *
1319662 GGAAAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAGTTCTTCTCATTATGAA
63 GGAAAAGCTAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAA
* *
1319727 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGTTGATCCAT
128 CTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGCTGATCCAT
1319791 TGTTATGGAT
Statistics
Matches: 167, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
220 16 0.10
221 7 0.04
222 91 0.54
223 2 0.01
224 2 0.01
226 49 0.29
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.39
Consensus pattern (223 bp):
TTCTTCTAATTATGAACTCTTCTTCTTCATATGACGAGTTCTTCTCATTATGAACTCTATCTGGA
AAAGCTAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
CTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGCTGATCCATCAATT
GATGAATTCAGGCAAAAGGTTGAACAAG
Found at i:1319686 original size:113 final size:112
Alignment explanation
Indices: 1319378--1319790 Score: 593
Period size: 113 Copynumber: 3.7 Consensus size: 112
1319368 AGATGACGAA
* * * * * *
1319378 TTCTTCTAATTATGAAC-TCTTCTTCTTCAT-ATGACGAGTTCTTCTGATTATGAACTCTATCTG
1 TTCTTCTCATTATGAACTTCTTCTTCTTCTTCA-GATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * ** *
1319441 GCAATGTTAATCCATCAATTGATGAATTTAAACAAAAGGTTGAACAAA
65 GAAATGCTGATCCATCAATTGATGAATTCAGGCAAAAGGTTGAACAAG
* *
1319489 TTCTTCTCATTATGAACTTC-T-TT-TTCTTCAGATGAGTTCTTTTCATTATGAACTTTTTCTGG
1 TTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
*
1319551 AAAGGCTGATCCATCAATTGATGAATTCAGGCAAAAGGTTGAACAAG
66 AAATGCTGATCCATCAATTGATGAATTCAGGCAAAAGGTTGAACAAG
1319598 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
1319663 GAAAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAG
65 GAAATGCTGATCCATCAATTGATGAATTCAGGCAAAAGGTTGAACAAG
1319711 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
1319776 GAAATGTTGATCCAT
65 GAAATGCTGATCCAT
1319791 TGTTATGGAT
Statistics
Matches: 275, Mismatches: 21, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
109 90 0.33
110 4 0.01
111 19 0.07
112 2 0.01
113 160 0.58
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.39
Consensus pattern (112 bp):
TTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
AAATGCTGATCCATCAATTGATGAATTCAGGCAAAAGGTTGAACAAG
Found at i:1320664 original size:115 final size:115
Alignment explanation
Indices: 1320491--1320921 Score: 738
Period size: 115 Copynumber: 3.8 Consensus size: 115
1320481 GATCATGCAG
* * * *
1320491 TTCATCTTTTAATTCCAATGATTGGTTCTGTAG-TTCCTACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
1320555 AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
66 AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
1320605 TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
1320670 AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
66 AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
*** *
1320720 TTCATCTTTCAAATTTGATGATTGGTTCTGTGGTTTCATATCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
*
1320785 AACACTTCCAGAAGATGCTATTGAGTTTCCTTATTTCTACTATGAGCAAA
66 AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
*** *
1320835 TTCATCTTTCAAATTTGATGATTGGTTCTGTGGTTTCATATCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
1320900 AACACTTCCAGAAGATGCTATT
66 AACACTTCCAGAAGATGCTATT
1320922 AGCACATTTA
Statistics
Matches: 307, Mismatches: 9, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
114 30 0.10
115 277 0.90
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (115 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
Found at i:1321024 original size:83 final size:83
Alignment explanation
Indices: 1320876--1321177 Score: 514
Period size: 83 Copynumber: 3.6 Consensus size: 83
1320866 GGTTTCATAT
* * *
1320876 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTTATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTAATCTTCCAAA
1320941 TTCAATGATTGGTTTTAC
66 TTCAATGATTGGTTTTAC
**
1320959 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTAATCTTCCAAA
1321024 TTCAATGATTGGTTTTAC
66 TTCAATGATTGGTTTTAC
* * *
1321042 CAAACCAGATCAGATAACTCAAAGACCACTTCTAGAAGATGCTATGAGCACATTATTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTAATCTTCCAAA
*
1321107 TTCAATGATTGATTTTAC
66 TTCAATGATTGGTTTTAC
*
1321125 CAAACCAGATCATATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACAT
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACAT
1321178 GGCATTTGTT
Statistics
Matches: 207, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 207 1.00
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.27
Consensus pattern (83 bp):
CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTAATCTTCCAAA
TTCAATGATTGGTTTTAC
Found at i:1322569 original size:15 final size:15
Alignment explanation
Indices: 1322551--1322619 Score: 72
Period size: 14 Copynumber: 4.7 Consensus size: 15
1322541 TTTCTTTTTT
1322551 CTTTTTTTTTCCTTC
1 CTTTTTTTTTCCTTC
*
1322566 C-TTTTTTTTCTTTTC
1 CTTTTTTTTTC-CTTC
* *
1322581 CTTTTTTTTT-ATTT
1 CTTTTTTTTTCCTTC
*
1322595 CTTTTTTTTTTCTT-
1 CTTTTTTTTTCCTTC
1322609 CTTTTTTTTTC
1 CTTTTTTTTTC
1322620 TTCAAGCATA
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
14 31 0.67
15 7 0.15
16 8 0.17
ACGTcount: A:0.01, C:0.17, G:0.00, T:0.81
Consensus pattern (15 bp):
CTTTTTTTTTCCTTC
Found at i:1322599 original size:44 final size:43
Alignment explanation
Indices: 1322537--1322621 Score: 134
Period size: 44 Copynumber: 2.0 Consensus size: 43
1322527 CCTTGACCCC
1322537 CCTTTTTCTTTTTTCTTTTTTTTTCCTTCCTTTTTTTTCTTTT
1 CCTTTTTCTTTTTTCTTTTTTTTTCCTTCCTTTTTTTTCTTTT
* * *
1322580 CCTTTTTTTTTATTTCTTTTTTTTTTCTTCTTTTTTTTTCTT
1 CCTTTTTCTTT-TTTCTTTTTTTTTCCTTCCTTTTTTTTCTT
1322622 CAAGCATAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
43 10 0.26
44 28 0.74
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (43 bp):
CCTTTTTCTTTTTTCTTTTTTTTTCCTTCCTTTTTTTTCTTTT
Found at i:1329967 original size:15 final size:16
Alignment explanation
Indices: 1329947--1329979 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1329937 TGAATGATGA
1329947 ATGTATGC-AAAATGT
1 ATGTATGCAAAAATGT
1329962 ATGTATGCAAAAATGT
1 ATGTATGCAAAAATGT
1329978 AT
1 AT
1329980 TGATCCCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.33
Consensus pattern (16 bp):
ATGTATGCAAAAATGT
Found at i:1335416 original size:3 final size:3
Alignment explanation
Indices: 1335408--1335476 Score: 93
Period size: 3 Copynumber: 23.0 Consensus size: 3
1335398 TATATATATT
* * * *
1335408 TAA TAA TAA TAA TAA TAA TAA TAG TAA TAT TTA TAA TAA TAA TAC TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1335456 TAA TAA TGA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
1335477 ATAAATAAAT
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1336563 original size:2 final size:2
Alignment explanation
Indices: 1336556--1336646 Score: 182
Period size: 2 Copynumber: 45.5 Consensus size: 2
1336546 GTGTATAAAC
1336556 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1336598 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1336640 TA TA TA T
1 TA TA TA T
1336647 GAATAGGTGT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 89 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1341292 original size:17 final size:17
Alignment explanation
Indices: 1341272--1341310 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
1341262 GAAAGAAAGT
*
1341272 TGGAGAGAGTGTGGTGG
1 TGGAGAGAGTGAGGTGG
1341289 TGGAGAGAGTGAGGTGG
1 TGGAGAGAGTGAGGTGG
1341306 TGGAG
1 TGGAG
1341311 TGCCGCGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.59, T:0.21
Consensus pattern (17 bp):
TGGAGAGAGTGAGGTGG
Found at i:1345305 original size:28 final size:22
Alignment explanation
Indices: 1345238--1345290 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
1345228 GAGCTCTCAA
1345238 AAAATGAAATTTGAAAGTATTG
1 AAAATGAAATTTGAAAGTATTG
1345260 AAAATGAAATTTGAAAGTATTG
1 AAAATGAAATTTGAAAGTATTG
1345282 AAAATGAAA
1 AAAATGAAA
1345291 ATTCGATTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.55, C:0.00, G:0.17, T:0.28
Consensus pattern (22 bp):
AAAATGAAATTTGAAAGTATTG
Found at i:1349193 original size:23 final size:23
Alignment explanation
Indices: 1349162--1349222 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
1349152 TAGTGCAGAG
* *
1349162 GGAATCGATACCCCCATTGAAGA
1 GGAACCGATTCCCCCATTGAAGA
* *
1349185 GGAACCGATTCCCCCTTTGAAGG
1 GGAACCGATTCCCCCATTGAAGA
1349208 GGAACCGATTCCCCC
1 GGAACCGATTCCCCC
1349223 CCACAGGGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.33, G:0.23, T:0.18
Consensus pattern (23 bp):
GGAACCGATTCCCCCATTGAAGA
Found at i:1361556 original size:38 final size:37
Alignment explanation
Indices: 1361499--1361587 Score: 135
Period size: 38 Copynumber: 2.4 Consensus size: 37
1361489 ACCCGAACCC
*
1361499 AACCCGACCTGACCTGACCCGAATATCACACTTAAAA
1 AACCCGACCCGACCTGACCCGAATATCACACTTAAAA
1361536 AACCCCGACCCGA-CTCGACCCGAATATCACACTTAAAA
1 AA-CCCGACCCGACCT-GACCCGAATATCACACTTAAAA
*
1361574 AACTCGACCCGACC
1 AACCCGACCCGACC
1361588 CGAACAAAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
37 13 0.28
38 34 0.72
ACGTcount: A:0.36, C:0.39, G:0.11, T:0.13
Consensus pattern (37 bp):
AACCCGACCCGACCTGACCCGAATATCACACTTAAAA
Found at i:1361834 original size:263 final size:262
Alignment explanation
Indices: 1361445--1362237 Score: 1170
Period size: 263 Copynumber: 3.0 Consensus size: 262
1361435 TATAAGGTAA
* *
1361445 AATTATATATATTTTTTGGGTCGGTCTGGTTTTTTTCACCCTAAACCCGAACCCAACCCGACCTG
1 AATTATATATA-TTTTTGGGTCGGTCCGGTTTTTTTCACCCTAAA-CCGAA-CCGACCCGA--T-
*
1361510 ACCTGACCCGAATATCACACTTAAAAAACCCCGACCCGACTCGACCCGAATATCACACTTAAAAA
60 -CC-GACCCGAATATCACACTTAAAAAAACCCGACCCGACTCGACCCGAATATCACACTTAAAAA
* * * * *
1361575 ACTCGACCCGACCCGAACAAAATAAAATTTCATTCAACCCAACCCGAATATATGAATTATAAATC
123 ACCCGACCCGACCCGAACAAAATAAAGTTTCATCCAACCCGACCCGAATATATGAATTAGAAATC
* * *
1361640 TGACCCGACCCGAACCGAAATAATAAAAAATTATTTTTATTTAATAAAACCAGTGACTTAATCCG
188 CGACCCGACCCGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCG
1361705 ACCCGACCCG
253 ACCCGACCCG
1361715 AATTATATATATTTTTGGGTCGGTCCGGTTTTTTTCACCCTAAACCGAACTCGACCCGATCCGAC
1 AATTATATATATTTTTGGGTCGGTCCGGTTTTTTTCACCCTAAACCGAAC-CGACCCGATCCGAC
* * *
1361780 CCGAATATCACTCTTAAAAAAAACCGACCCGACTCGACCCGAATATCTCACTTAAAAAACCCGAC
65 CCGAATATCACACTTAAAAAAACCCGACCCGACTCGACCCGAATATCACACTTAAAAAACCCGAC
* * * * *
1361845 CCGATCCGAACAAAATAAAGTTTCATCCGACCCGACCCAAATATATGAATTAGAAATCCGATCTG
130 CCGACCCGAACAAAATAAAGTTTCATCCAACCCGACCCGAATATATGAATTAGAAATCCGACCCG
1361910 ACCCGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGAC
195 ACCCGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGAC
1361975 CCG
260 CCG
*
1361978 AATTATATATATTTTTGGGTCGGTCCGGTTTTTTTCACCCTAAA-C---CCGA----ACCCGACC
1 AATTATATATATTTTTGGGTCGGTCCGGTTTTTTTCACCCTAAACCGAACCGACCCGATCCGACC
*
1362035 CGAATATCACACTTAAAAAAACCCGACCCGAATCGACCCGAATATCACACTTAAAAAACCCGACC
66 CGAATATCACACTTAAAAAAACCCGACCCGACTCGACCCGAATATCACACTTAAAAAACCCGACC
* *
1362100 CAACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGACCCGAATATATGAATTAGAAATCCAA
131 CGACCCGAACAAAATAAAGTTTCATCC-A----ACCCGACCCGAATATATGAATTAGAAATCCGA
* * *
1362165 CCCAATCCGACCCGAAATAATAAAAAAGTATTTTTATTTAATAAAAACAGTGACTTAATCCGACC
191 CCCGACCCGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGACC
1362230 CGACCCG
256 CGACCCG
1362237 A
1 A
1362238 CCCGAATATC
Statistics
Matches: 483, Mismatches: 34, Indels: 23
0.89 0.06 0.04
Matches are distributed among these distances:
254 93 0.19
258 3 0.01
259 99 0.20
262 1 0.00
263 228 0.47
264 2 0.00
266 1 0.00
267 1 0.00
268 12 0.02
269 32 0.07
270 11 0.02
ACGTcount: A:0.37, C:0.28, G:0.12, T:0.23
Consensus pattern (262 bp):
AATTATATATATTTTTGGGTCGGTCCGGTTTTTTTCACCCTAAACCGAACCGACCCGATCCGACC
CGAATATCACACTTAAAAAAACCCGACCCGACTCGACCCGAATATCACACTTAAAAAACCCGACC
CGACCCGAACAAAATAAAGTTTCATCCAACCCGACCCGAATATATGAATTAGAAATCCGACCCGA
CCCGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACC
CG
Found at i:1361846 original size:37 final size:38
Alignment explanation
Indices: 1361766--1361853 Score: 126
Period size: 38 Copynumber: 2.3 Consensus size: 38
1361756 AAACCGAACT
*
1361766 CGACCCGATCCGACCCGAATATCACTCTTAAAAAAAAC
1 CGACCCGATCCGACCCGAATATCACACTTAAAAAAAAC
* *
1361804 CGACCCGA-CTCGACCCGAATATCTCACTT-AAAAAACC
1 CGACCCGATC-CGACCCGAATATCACACTTAAAAAAAAC
1361841 CGACCCGATCCGA
1 CGACCCGATCCGA
1361854 ACAAAATAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
37 19 0.42
38 26 0.58
ACGTcount: A:0.35, C:0.38, G:0.12, T:0.15
Consensus pattern (38 bp):
CGACCCGATCCGACCCGAATATCACACTTAAAAAAAAC
Found at i:1362075 original size:38 final size:38
Alignment explanation
Indices: 1362021--1362107 Score: 142
Period size: 38 Copynumber: 2.3 Consensus size: 38
1362011 TTCACCCTAA
1362021 ACCCGAACCCGACCCGAATATCACACTTAAAAAAACCCG
1 ACCCGAACCCGACCCGAATATCACACTT-AAAAAACCCG
*
1362060 ACCCGAA-TCGACCCGAATATCACACTTAAAAAACCCG
1 ACCCGAACCCGACCCGAATATCACACTTAAAAAACCCG
1362097 ACCC-AACCCGA
1 ACCCGAACCCGA
1362108 ACAAAATAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
36 2 0.04
37 17 0.38
38 19 0.42
39 7 0.16
ACGTcount: A:0.40, C:0.39, G:0.10, T:0.10
Consensus pattern (38 bp):
ACCCGAACCCGACCCGAATATCACACTTAAAAAACCCG
Found at i:1362248 original size:167 final size:156
Alignment explanation
Indices: 1362057--1362363 Score: 427
Period size: 167 Copynumber: 1.9 Consensus size: 156
1362047 TTAAAAAAAC
*
1362057 CCGACCCGAATCGACCCGAATATCACACTT-AAAAAACCCGACCCAACCCGAACAAAATAAAGTT
1 CCGACCCGAACCGACCCGAATATCACACTTAAAAAAACCCGACCCAACCCGAACAAAATAAAG-T
*
1362121 TCATCCGACCCGACCCGACCCGAATATATGAATTAGAAATCCAACCCAATCCGACCCGAAATAAT
65 T--T-C-ACCCGACCCGACCCGAATATATGAATTAG--A---AACCCAACCCGACCCGAAATAAT
*
1362186 AAAAAAGTATTTTTATTTAATAAAAACAGTGACTTAAT
121 -AAAAA-TATTTTTATTCAATAAAAACAGTGACTTAAT
* * * *
1362224 CCGACCCGACCCGACCCGAATATCACACTTAAAAAAACCCGATCCGACCCGACCAAAATAAAGTT
1 CCGACCCGAACCGACCCGAATATCACACTTAAAAAAACCCGACCCAACCCGAACAAAATAAAGTT
*
1362289 TCACCCGACCCGACCCGAATATATGAATTAGAAACCCGACCCGACCCGAAATAATAAAAATATTT
66 TCACCCGACCCGACCCGAATATATGAATTAGAAACCCAACCCGACCCGAAATAATAAAAATATTT
1362354 TTATTCAATA
131 TTATTCAATA
1362364 TATGAATAAG
Statistics
Matches: 131, Mismatches: 8, Indels: 13
0.86 0.05 0.09
Matches are distributed among these distances:
156 14 0.11
157 5 0.04
158 21 0.16
161 1 0.01
163 29 0.22
164 1 0.01
165 1 0.01
167 30 0.23
168 29 0.22
ACGTcount: A:0.41, C:0.29, G:0.11, T:0.19
Consensus pattern (156 bp):
CCGACCCGAACCGACCCGAATATCACACTTAAAAAAACCCGACCCAACCCGAACAAAATAAAGTT
TCACCCGACCCGACCCGAATATATGAATTAGAAACCCAACCCGACCCGAAATAATAAAAATATTT
TTATTCAATAAAAACAGTGACTTAAT
Found at i:1363165 original size:82 final size:81
Alignment explanation
Indices: 1363079--1363229 Score: 212
Period size: 82 Copynumber: 1.9 Consensus size: 81
1363069 TATTATGGTG
* * * * * **
1363079 TTTGTATGAAAACGCCTCTAAATTACTTTCTTTTATGGCGTTTGTTGTAACGACACCACTATATA
1 TTTGTATGAAAACGCCGCTAAATTACTTTATGTTACGACGTTTGTTG-AAAAACACCACTATATA
1363144 TGAACATTATTGCAGTA
65 TGAACATTATTGCAGTA
* *
1363161 TTTGTATGAAAATGCCGCTAAATTACTTTATGTTGCGACGTTTGTTGAAAAACACCACTATATAT
1 TTTGTATGAAAACGCCGCTAAATTACTTTATGTTACGACGTTTGTTGAAAAACACCACTATATAT
1363226 GAAC
66 GAAC
1363230 CCTATTGTGG
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
81 20 0.33
82 40 0.67
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (81 bp):
TTTGTATGAAAACGCCGCTAAATTACTTTATGTTACGACGTTTGTTGAAAAACACCACTATATAT
GAACATTATTGCAGTA
Found at i:1364570 original size:24 final size:24
Alignment explanation
Indices: 1364537--1364611 Score: 89
Period size: 24 Copynumber: 3.1 Consensus size: 24
1364527 GTTCGTGAAC
* * *
1364537 GTTCGATTATGTTTGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGATTAT
*
1364561 GTTTGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTCGATTAT
*
1364585 GTTCGTTTATGTTCATTC-ATTTAT
1 GTTCGTTTATGTTCGTTCGA-TTAT
1364609 GTT
1 GTT
1364612 TAACTCAATC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
23 1 0.02
24 43 0.98
ACGTcount: A:0.13, C:0.09, G:0.20, T:0.57
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGATTAT
Found at i:1364588 original size:14 final size:14
Alignment explanation
Indices: 1364536--1364591 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 14
1364526 CGTTCGTGAA
1364536 CGTTCGATTATGTT
1 CGTTCGATTATGTT
* *
1364550 TGTTCGGTTATG-T
1 CGTTCGATTATGTT
*
1364563 --TT-GTTTATGTT
1 CGTTCGATTATGTT
1364574 CGTTCGATTATGTT
1 CGTTCGATTATGTT
1364588 CGTT
1 CGTT
1364592 TATGTTCATT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
10 6 0.18
11 3 0.09
13 3 0.09
14 22 0.65
ACGTcount: A:0.11, C:0.11, G:0.23, T:0.55
Consensus pattern (14 bp):
CGTTCGATTATGTT
Found at i:1365345 original size:10 final size:10
Alignment explanation
Indices: 1365330--1365404 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
1365320 GGGTCTCCAA
1365330 CGTTTATGTT
1 CGTTTATGTT
1365340 CGTTTATGTT
1 CGTTTATGTT
1365350 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
1365361 ATGTTCGTGTT
1 -CGTTTATGTT
1365372 CGTTTATGTT
1 CGTTTATGTT
1365382 CG----TGTT
1 CGTTTATGTT
1365388 CGTTTATGTT
1 CGTTTATGTT
1365398 CGTTTAT
1 CGTTTAT
1365405 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:1365361 original size:16 final size:16
Alignment explanation
Indices: 1365336--1365400 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
1365326 CCAACGTTTA
1365336 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
1365352 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
1365368 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1365384 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1365400 T
1 T
1365401 TTATTTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1365491 original size:16 final size:16
Alignment explanation
Indices: 1365470--1365502 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1365460 AAAAAAATTT
1365470 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1365486 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1365502 T
1 T
1365503 CTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1366238 original size:18 final size:18
Alignment explanation
Indices: 1366217--1366252 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1366207 CTTTAGATAC
*
1366217 AAGATATGCCTTATACAT
1 AAGATATACCTTATACAT
1366235 AAGATATACCTTATACAT
1 AAGATATACCTTATACAT
1366253 GTCAACATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (18 bp):
AAGATATACCTTATACAT
Found at i:1367984 original size:515 final size:514
Alignment explanation
Indices: 1367012--1368043 Score: 1601
Period size: 515 Copynumber: 2.0 Consensus size: 514
1367002 TTTTCAAATG
* *
1367012 AGTACTTTCAAACTTATTATGCTTCGACCTTTCTTCCTCTTACACACAATAAAAAATGAGCTCAT
1 AGTACTTTCAAACTTATTATGCTTCAACATTTCTTCCTCTTACACACAATAAAAAATGAGCTCAT
* * *
1367077 TTAGAGTTCATTTCTTCCTTTCAGTTGATTAAACTCTATATGAAGCGATACCGAAATCATAAGAA
66 TTAGAGTTCATTTCTCCCTTTCAGTTGATTAAACTCTATAGGAAGCGATACCGAAATCACAAGAA
1367142 CAAGTAATTCTTATAAAAAAACTCGAGCTTAAGTGTCGTAAGTCTTGAAGCAATTTGAAACATAT
131 CAAGTAATTCTTATAAAAAAACTCGAGCTTAAGTGTCGTAAGTCTTGAAGCAATTTGAAACATAT
* *
1367207 TCATAATGTACTCCCTTATATTTCATTAACTTGTATACTTTATAGGCATACAAAAAAGTTAAAAG
196 TCATAATGTACTCCCTTACATTTCATTAACTTGTATACTTTATAGGCATACAAAAAAGTCAAAAG
1367272 TCATGTCATAAACATTATTTTTTTAGGAAAACATTTCTCAATTTCGTCAAGGAAACCATTGGCTT
261 TCATGTCATAAACATTATTTTTTTAGGAAAACATTTCTCAATTTCGTCAAGGAAACCATTGGCTT
* *
1367337 GAATAATCTTTTTAGATTATGTGCCCCTAAAGGCTAAAAAAATATTGTTACTTCATGACTACTAG
326 GAATAATCTTTTTAGATTATGTGCCCCTAAAGGATAAAAAAATATTGTTACTTCATGACCACTAG
1367402 ACTCATGCAATTTGAATAAATTTCACCTCTCAAAATCTGTTATACCAATTGAGGATGTTATTCCC
391 ACTCATGCAATTTGAATAAATTTCACCTCTCAAAATCTGTTATACCAATTGAGGATGTTATTCCC
* * * *
1367467 CATGAGAGGTGGAATTGTTTTTAGTGCAAAGTCTATGTTCATACAACCAAAACCTTATGTA
456 CATAAGAGGTGGAA-T-TATTTAGTGCAAAGTCTATATTCATACAAACAAAACCTTATGTA
* * *
1367528 AGTACTTTCAGACTTATTATGTTTCAACATTTCTTCCTC-TAGCACATAATAAAAAATGAGCTCA
1 AGTACTTTCAAACTTATTATGCTTCAACATTTCTTCCTCTTA-CACACAATAAAAAATGAGCTCA
* *
1367592 TTTAGAGTTCATTTCTCCCTTTCAGTTGATTAAACTCTATAGGAAGCGATACTGAAATCACAATA
65 TTTAGAGTTCATTTCTCCCTTTCAGTTGATTAAACTCTATAGGAAGCGATACCGAAATCACAAGA
* *
1367657 ACACA-TAATTC-T-TAAAAAAACTTGAGCTTAAGT-TCCTTAAGTCTTGAAGCAATTTGAAACA
130 ACA-AGTAATTCTTATAAAAAAACTCGAGCTTAAGTGT-CGTAAGTCTTGAAGCAATTTGAAACA
* * * * *
1367718 TATTCTTAATGTACTCCCTTACATTTCCTTGACTCT-TATATTTTATAGGCATA-AAATAAGTCA
193 TATTCATAATGTACTCCCTTACATTTCATTAACT-TGTATACTTTATAGGCATACAAAAAAGTCA
* * * * * *
1367781 AAAGTGATGTCATATACCTTATTTTTTTTTGGGAAATCATTTCTCAATTTTGTCAAGGAAACCAT
257 AAAGTCATGTCATAAACATTA--TTTTTTTAGGAAAACATTTCTCAATTTCGTCAAGGAAACCAT
* * * *
1367846 TGGCTTGAATAATCTTTTTAGATTATGTTCCCTTAAAGGATGAAAAAATGTTGTTACTTCATGAC
320 TGGCTTGAATAATCTTTTTAGATTATGTGCCCCTAAAGGATAAAAAAATATTGTTACTTCATGAC
*
1367911 CACTAGACTCATGCAATTTGAATAAATTTCGCCTCTCAAAATCTGTTATACCAATTGAGGATGTT
385 CACTAGACTCATGCAATTTGAATAAATTTCACCTCTCAAAATCTGTTATACCAATTGAGGATGTT
* *
1367976 ATTCCCCATAAGAGGTGGAATTATTTAGTGCAAAGTCTATATTCATATAAACTAAACCTTATGTA
450 ATTCCCCATAAGAGGTGGAATTATTTAGTGCAAAGTCTATATTCATACAAACAAAACCTTATGTA
1368041 AGT
1 AGT
1368044 GCATTTTTCC
Statistics
Matches: 472, Mismatches: 38, Indels: 15
0.90 0.07 0.03
Matches are distributed among these distances:
513 69 0.15
514 92 0.19
515 185 0.39
516 125 0.26
517 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (514 bp):
AGTACTTTCAAACTTATTATGCTTCAACATTTCTTCCTCTTACACACAATAAAAAATGAGCTCAT
TTAGAGTTCATTTCTCCCTTTCAGTTGATTAAACTCTATAGGAAGCGATACCGAAATCACAAGAA
CAAGTAATTCTTATAAAAAAACTCGAGCTTAAGTGTCGTAAGTCTTGAAGCAATTTGAAACATAT
TCATAATGTACTCCCTTACATTTCATTAACTTGTATACTTTATAGGCATACAAAAAAGTCAAAAG
TCATGTCATAAACATTATTTTTTTAGGAAAACATTTCTCAATTTCGTCAAGGAAACCATTGGCTT
GAATAATCTTTTTAGATTATGTGCCCCTAAAGGATAAAAAAATATTGTTACTTCATGACCACTAG
ACTCATGCAATTTGAATAAATTTCACCTCTCAAAATCTGTTATACCAATTGAGGATGTTATTCCC
CATAAGAGGTGGAATTATTTAGTGCAAAGTCTATATTCATACAAACAAAACCTTATGTA
Found at i:1372802 original size:10 final size:10
Alignment explanation
Indices: 1372787--1372811 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1372777 GTTTTACTTG
1372787 TTTGTTTTCT
1 TTTGTTTTCT
1372797 TTTGTTTTCT
1 TTTGTTTTCT
1372807 TTTGT
1 TTTGT
1372812 AGGTTTTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.12, T:0.80
Consensus pattern (10 bp):
TTTGTTTTCT
Found at i:1385054 original size:29 final size:23
Alignment explanation
Indices: 1384993--1385045 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
1384983 GGATGATGTT
1384993 GATGGTGTTGAAGATGAAATGGA
1 GATGGTGTTGAAGATGAAATGGA
1385016 GATGGTGTTGAAGATGAAATGGA
1 GATGGTGTTGAAGATGAAATGGA
1385039 GATGGTG
1 GATGGTG
1385046 GTGATGTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.32, C:0.00, G:0.42, T:0.26
Consensus pattern (23 bp):
GATGGTGTTGAAGATGAAATGGA
Found at i:1390219 original size:14 final size:14
Alignment explanation
Indices: 1390183--1390226 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
1390173 TTTCCTCGGC
*
1390183 TTTTCTTTT-TTTT
1 TTTTCTTTTCTTCT
**
1390196 TTTTAATTTCTTCT
1 TTTTCTTTTCTTCT
1390210 TTTTCTTTTCTTCT
1 TTTTCTTTTCTTCT
1390224 TTT
1 TTT
1390227 CTGAATTATT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 7 0.28
14 18 0.72
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTCTTTTCTTCT
Found at i:1402195 original size:65 final size:62
Alignment explanation
Indices: 1402114--1402258 Score: 168
Period size: 61 Copynumber: 2.3 Consensus size: 62
1402104 GCAAGTTTAT
* * *
1402114 ATTAGCACTAGTGTGTAAGGACACTAAGCGCAGGTGGTGGGCAC-AATCTTATGTGTCATATCCG
1 ATTAGCACTAGAGTGTAA-GAC-CT-AGCGCAGGGGGTGGGC-CTAAACTTATGTGTCATATCCG
1402178 G
62 G
* *
1402179 ATTAGCACTAGAGTGTAA-ACCTAGTGTAGGGGGTGGGCCTAAACTTATGTGTCATATCCGG
1 ATTAGCACTAGAGTGTAAGACCTAGCGCAGGGGGTGGGCCTAAACTTATGTGTCATATCCGG
* * *
1402240 ATTAGAAGTAGAGCGTAAG
1 ATTAGCACTAGAGTGTAAG
1402259 TTCAATGCAG
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
60 1 0.01
61 48 0.69
62 2 0.03
63 2 0.03
65 17 0.24
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.26
Consensus pattern (62 bp):
ATTAGCACTAGAGTGTAAGACCTAGCGCAGGGGGTGGGCCTAAACTTATGTGTCATATCCGG
Found at i:1405839 original size:961 final size:954
Alignment explanation
Indices: 1404110--1406021 Score: 3497
Period size: 961 Copynumber: 2.0 Consensus size: 954
1404100 CTAACCCTAA
* *
1404110 TTAACCTTACCAATCATTGAATCAAATAATCGAAATGAACCTTCGAGCATCTAAATGAGAGATCC
1 TTAACCTTACCAATCATTGAATCAAATAATCGAAATGAACATTCGAGCATCTAAATGAGAGATAC
1404175 AAATTGAATTATTCCCTAAATTAGACTAAATGAATCTAACTAATGTAGAGGTTTTTAACATTAAT
66 AAATTGAATTATTCCCTAAATTAGACTAAATGAATCTAACTAATGTAGAGGTTTTTAACATTAAT
1404240 CTAAATTAATTTTAATCAATATTGCAATTCGAATAATTAAAGTGGAACCTCGAGCAAAGCGGTGA
131 CTAAATTAATTTTAATCAATATTGCAATTCGAATAATTAAAGTGGAACCTCGAGCAAAGCGGTGA
1404305 CCAAATTAAGAATTCTCCTAACTTAAAGATTAATATGAAATTAGGCCTAATTTGGAGATAATCAT
196 CCAAATTAAGAATTCTCCTAACTTAAAGATTAATATGAAATTAGGCCTAATTTGGAGATAATCAT
*
1404370 GTACCCAATAACCGGACATTGTCTTATTTTGGAAATCATGATGCGGTCTTGAAAAGATGTCGAAC
261 GTACCCAATAACCGGACATTGTCTTATTTTAGAAATCATGATGCGGTCTTGAAAAGATGTCGAAC
1404435 TATTTCGAGAATCACCATAGTCACCCCTTGAACATACTTGCGGGAGATATACTATCAATCCCTAA
326 TATTTCGAGAATCACCATAGTCACCCCTTGAACATACTTGCGGGAGATATACTATCAATCCCTAA
*
1404500 TAATGAACAATACCTTAAATTTTGAAATAAAGAGAATCAAACAATTTTTTATTATCCTAATTAAA
391 TAATGAACAATACCTTAAATTTTGAAATAAAGAGAATCAAACAAATTTTTATTATCCTAATTAAA
1404565 CTAAGGATATATTAGGTTTTCTCTAGCTTACAGTATCAACTATGATAATTAAGAACCTAGAGGCA
456 CTAAGGATATATTAGGTTTTCTCTAGCTTACAGTATCAACTATGATAATTAAGAACCTAGAGGCA
1404630 TAAACCTAAAAATGTAGGCTCTAATATGAATCCTACTTGATTTTAACCAGTTTATTGAATCGAAT
521 TAAACCTAAAAATGTAGGCTCTAATATGAATCCTACTTGATTTTAACCAGTTTATTGAATCGAAT
1404695 AATTGAGATGGTCCCTTGTGCCTTTATAAGGGCCAACTCAATTACACTCTAAATTGAAGGGTCTA
586 AATTGAGATGGTCCCTTGTGCCTTTATAAGGGCCAACTCAATTACACTCTAAATTGAAGGGTCTA
1404760 AATTGAAATCTAATCGAAAGTGGAGGCTCTAATTGTCCATCTAATCAATTATGTCAAAAGGATAA
651 AATTGAAATCTAATCGAAAGTGGAGGCTCTAATTGTCCATCTAATCAATTATGTCAAAAGGATAA
1404825 TCTAGTTAAAAGTTTAGGGATTAGAATGTGAGAAGCCAAGATTAAGGCTCTAATTACTAACCCTA
716 TCTAGTTAAAAGTTTAGGGATTAGAATGTGAGAAGCCAAGATTAAGGCTCTAATTACTAACCCTA
*
1404890 ATTAACCTTACCAATCATTGAATC-AATAATCGAAATGAACATTCGAGCATCTAAATGAGAGATA
781 ATTAACCTTACCAATCATTGAATCAAATAATCGAAATGAAC-CTCGAGCATCTAAATGAGAGATA
1404954 CAAATTGAATTATTCCCT-AATTAGACTAAAATG-AATCTAACTAATGTA-AGGTTTTAACATTA
845 CAAATTGAATTATTCCCTAAATTAGACTAAAATGAAATCTAACTAATGTAGAGGTTTTAACATTA
1405016 ATCTAAA-TAATTTTAATC-ATATTGCAATTCGAATAATTAAGTG
910 ATCTAAATTAATTTTAATCAATATTGCAATTCGAATAATTAAGTG
1405059 TTAACCTTACCAATCATTGAATCAAATAATCGAAATGAACATTCGAGCATCTAAATGAGAGATAC
1 TTAACCTTACCAATCATTGAATCAAATAATCGAAATGAACATTCGAGCATCTAAATGAGAGATAC
1405124 AAATTGAATTATTCCCTAAATTAGACTAAAATGAAATCTAACTAATGTAGAGG-TTTTAACATTA
66 AAATTGAATTATTCCCTAAATTAGACT-AAATG-AATCTAACTAATGTAGAGGTTTTTAACATTA
1405188 ATCTAAATTAATTTTAATCAATATTGCAATTCGAATAATTAAAGTGGAACCTCGAGCAAAAGCGG
129 ATCTAAATTAATTTTAATCAATATTGCAATTCGAATAATTAAAGTGGAACCTCGAGC-AAAGCGG
1405253 TGACCAAATTAAGAATTCTCCTAACTTAAAGATTAAATATGAAATTAGGCCTAATTTGGAGATAA
193 TGACCAAATTAAGAATTCTCCTAACTTAAAGATT-AATATGAAATTAGGCCTAATTTGGAGATAA
1405318 TCATTGTACCCAATAACCGGACATTGTCTTAATTTTAGAAATCATGATGCGGTCTTGAAAAGGAT
257 TCA-TGTACCCAATAACCGGACATTGTCTT-ATTTTAGAAATCATGATGCGGTCTTGAAAA-GAT
1405383 GTCGAACTATTTCGAGAATCACCAGTAGTCACCCCTTGAACATACTTGCGGGAGATATACTATCA
319 GTCGAACTATTTCGAGAATCACCA-TAGTCACCCCTTGAACATACTTGCGGGAGATATACTATC-
* *
1405448 AATCCCTAATAAATGAA-TATACCTTAAATTTTGAAATAAAG-GCAATCAAATAAATTTTTATTA
382 AATCCCTAAT-AATGAACAATACCTTAAATTTTGAAATAAAGAG-AATCAAACAAATTTTTATT-
1405511 ATCCTAATTAAACTAAGGATATATTAAGGTTTTCTCTAGCTTACAGTATCAAACTATGATAATTA
444 ATCCTAATTAAACTAAGGATATATT-AGGTTTTCTCTAGCTTACAGTATC-AACTATGATAATT-
1405576 AAGAACCTAGAGGCATAAACCT-AAAATGTAGGCTCTAATATGAATCCTACTTGATTTTAACCAG
506 AAGAACCTAGAGGCATAAACCTAAAAATGTAGGCTCTAATATGAATCCTACTTGATTTTAACCAG
1405640 -TTATTGAATCGAATAATTGAGATGGTCCCTTGTGCCTTTAGATAAGGGCCAACTCGAATTACAC
571 TTTATTGAATCGAATAATTGAGATGGTCCCTTGTGCCTTT--ATAAGGGCCAACTC-AATTACAC
1405704 TCTAAATTGAAGGGTCTAAATTGAAATCTAATCGAAAGTGGAGGCTCTAATTGTCCATCTAATCA
633 TCTAAATTGAAGGGTCTAAATTGAAATCTAATCGAAAGTGGAGGCTCTAATTGTCCATCTAATCA
1405769 ATTATGTC-AAAGGATAATCTAGTTAAAAGTTTAGGGATTAGAATGTGAGAAGCCAAGATTAAGG
698 ATTATGTCAAAAGGATAATCTAGTTAAAAGTTTAGGGATTAGAATGTGAGAAGCCAAGATTAAGG
1405833 CTCTAATTACTAACCCTAATTAACCTTACCAATCATTGAATCAAATAATCGAAATGAACCTCGAG
763 CTCTAATTACTAACCCTAATTAACCTTACCAATCATTGAATCAAATAATCGAAATGAACCTCGAG
*
1405898 CATCTAAATGAGAGATCCAAATTGAATTATTCCCTAAATTAGACTAAAATGAAATCTAACTAATG
828 CATCTAAATGAGAGATACAAATTGAATTATTCCCTAAATTAGACTAAAATGAAATCTAACTAATG
1405963 TAGAGGTTTTAACATTAATCTAAATTAATTTTAATCAATATTGCAATTCGAATAATTAA
893 TAGAGGTTTTAACATTAATCTAAATTAATTTTAATCAATATTGCAATTCGAATAATTAA
1406022 AGTGGAACCT
Statistics
Matches: 931, Mismatches: 8, Indels: 31
0.96 0.01 0.03
Matches are distributed among these distances:
949 90 0.10
950 73 0.08
951 60 0.06
952 33 0.04
953 26 0.03
954 29 0.03
955 27 0.03
956 40 0.04
957 50 0.05
958 31 0.03
959 63 0.07
960 55 0.06
961 173 0.19
962 112 0.12
963 15 0.02
964 21 0.02
965 11 0.01
966 22 0.02
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (954 bp):
TTAACCTTACCAATCATTGAATCAAATAATCGAAATGAACATTCGAGCATCTAAATGAGAGATAC
AAATTGAATTATTCCCTAAATTAGACTAAATGAATCTAACTAATGTAGAGGTTTTTAACATTAAT
CTAAATTAATTTTAATCAATATTGCAATTCGAATAATTAAAGTGGAACCTCGAGCAAAGCGGTGA
CCAAATTAAGAATTCTCCTAACTTAAAGATTAATATGAAATTAGGCCTAATTTGGAGATAATCAT
GTACCCAATAACCGGACATTGTCTTATTTTAGAAATCATGATGCGGTCTTGAAAAGATGTCGAAC
TATTTCGAGAATCACCATAGTCACCCCTTGAACATACTTGCGGGAGATATACTATCAATCCCTAA
TAATGAACAATACCTTAAATTTTGAAATAAAGAGAATCAAACAAATTTTTATTATCCTAATTAAA
CTAAGGATATATTAGGTTTTCTCTAGCTTACAGTATCAACTATGATAATTAAGAACCTAGAGGCA
TAAACCTAAAAATGTAGGCTCTAATATGAATCCTACTTGATTTTAACCAGTTTATTGAATCGAAT
AATTGAGATGGTCCCTTGTGCCTTTATAAGGGCCAACTCAATTACACTCTAAATTGAAGGGTCTA
AATTGAAATCTAATCGAAAGTGGAGGCTCTAATTGTCCATCTAATCAATTATGTCAAAAGGATAA
TCTAGTTAAAAGTTTAGGGATTAGAATGTGAGAAGCCAAGATTAAGGCTCTAATTACTAACCCTA
ATTAACCTTACCAATCATTGAATCAAATAATCGAAATGAACCTCGAGCATCTAAATGAGAGATAC
AAATTGAATTATTCCCTAAATTAGACTAAAATGAAATCTAACTAATGTAGAGGTTTTAACATTAA
TCTAAATTAATTTTAATCAATATTGCAATTCGAATAATTAAGTG
Found at i:1407369 original size:797 final size:796
Alignment explanation
Indices: 1405059--1407982 Score: 5547
Period size: 797 Copynumber: 3.7 Consensus size: 796
1405049 TAATTAAGTG
1405059 TTAACCTTACCAATCATTGAATCAAATAATCGAAATGAACATTCGAGCATCTAAATGAGAGATAC
1 TTAACCTTACCAATCATTGAATCAAATAATCGAAATGAACATTCGAGCATCTAAATGAGAGATAC
1405124 AAATTGAATTATTCCCTAAATTAGACTAAAATGAAATCTAACTAATGTAGAGGTTTTAACATTAA
66 AAATTGAATTATTCCCTAAATTAGACTAAAATGAAATCTAACTAATGTAGAGGTTTTAACATTAA
1405189 TCTAAATTAATTTTAATCAATATTGCAATTCGAATAATTAAAGTGGAACCTCGAGCAAAAGCGGT
131 TCTAAATTAATTTTAATCAATATTGCAATTCGAATAATTAAAGTGGAACCTCGAGCAAAAGCGGT
1405254 GACCAAATTAAGAATTCTCCTAACTTAAAGATTAAATATGAAATTAGGCCTAATTTGGAGATAAT
196 GACCAAATTAAGAATTCTCCTAACTTAAAGATTAAATATGAAATTAGGCCTAATTTGGAGATAAT
*
1405319 CATTGTACCCAATAACCGGACATTGTCTTAATTTTAGAAATCATGATGCGGTCTTGAAAAGGATG
261 CATTGTACCCAATAACCGGACATTGTCTTAATTTTAGAAATCATGATGCGGTCTTGAAAAAGATG
1405384 TCGAACTATTTCGAGAATCACCAGTAGTCACCCCTTGAACATACTTGCGGGAGATATACTATCAA
326 TCGAACTATTTCGAGAATCACCAGTAGTCACCCCTTGAACATACTTGCGGGAGATATACTATCAA
*
1405449 ATCCCTAATAAATGAA-TATACCTTAAATTTTGAAATAAAGGCAATCAAATAAATTTTTATTAAT
391 ATCCCTAATAAATGAACAATACCTTAAATTTTGAAATAAAGGCAATCAAATAAATTTTTATTAAT
1405513 CCTAATTAAACTAAGGATATATTAAGGTTTTCTCTAGCTTACAGTATCAAACTATGATAATTAAA
456 CCTAATTAAACTAAGGATATATTAAGGTTTTCTCTAGCTTACAGTATCAAACTATGATAATTAAA
1405578 GAACCTAGAGGCATAAACCT-AAAATGTAGGCTCTAATATGAATCCTACTTGATTTTAACCAGTT
521 GAACCTAGAGGCATAAACCTAAAAATGTAGGCTCTAATATGAATCCTACTTGATTTTAACCAGTT
*
1405642 ATTGAATCGAATAATTGAGATGGTCCCTTGTGCCTTTAGATAAGGGCCAACTCGAATTACACTCT
586 ATTGAATCGAATAATTGAGATGGTCCCTTGTGCCTTTAGATAAGGGCCAACTCAAATTACACTCT
1405707 AAATTGAAGGGTCTAAATTGAAATCTAATCGAAAGTGGAGGCTCTAATTGTCCATCTAATCAATT
651 AAATTGAAGGGTCTAAATTGAAATCTAATCGAAAGTGGAGGCTCTAATTGTCCATCTAATCAATT
1405772 ATGTC-AAAGGATAATCTAGTTAAAAGTTTAGGGATTAGAATGTGAGAAGCCAAGATTAAGGCTC
716 ATGTCAAAAGGATAATCTAGTTAAAAGTTTAGGGATTAGAATGTGAGAAGCCAAGATTAAGGCTC
1405836 TAATTACTAACCCTAA
781 TAATTACTAACCCTAA
* *
1405852 TTAACCTTACCAATCATTGAATCAAATAATCGAAATGAAC-CTCGAGCATCTAAATGAGAGATCC
1 TTAACCTTACCAATCATTGAATCAAATAATCGAAATGAACATTCGAGCATCTAAATGAGAGATAC
1405916 AAATTGAATTATTCCCTAAATTAGACTAAAATGAAATCTAACTAATGTAGAGGTTTTAACATTAA
66 AAATTGAATTATTCCCTAAATTAGACTAAAATGAAATCTAACTAATGTAGAGGTTTTAACATTAA
1405981 TCTAAATTAATTTTAATCAATATTGCAATTCGAATAATTAAAGTGGAACCTCGAGCAAAAGCGGT
131 TCTAAATTAATTTTAATCAATATTGCAATTCGAATAATTAAAGTGGAACCTCGAGCAAAAGCGGT
*
1406046 GACC-AATTAAGAATTCTCCTAACTTAAAAATTAAATATG-AATTAGGCCTAA-TTGGAGATAAT
196 GACCAAATTAAGAATTCTCCTAACTTAAAGATTAAATATGAAATTAGGCCTAATTTGGAGATAAT
*
1406108 CATTGTACCCAATAACCGGACATTGTCTTAATTTTGGAAATCATGATGCGGTCTTG-AAAAGATG
261 CATTGTACCCAATAACCGGACATTGTCTTAATTTTAGAAATCATGATGCGGTCTTGAAAAAGATG
1406172 TCGAACTATTTCGAGAATCACCAGTAGTCACCCCTTGAACATACTTGCGGGAGATATACTATCAA
326 TCGAACTATTTCGAGAATCACCAGTAGTCACCCCTTGAACATACTTGCGGGAGATATACTATCAA
* *
1406237 ATCCCTAAT-AATGAACAATACCTTAAATTTTGAAATAAA-G-AGATCAAACAATTTTTTATTAA
391 ATCCCTAATAAATGAACAATACCTTAAATTTTGAAATAAAGGCA-ATCAAATAAATTTTTATTAA
1406299 TCCTAA-T-AACTAAGGATATATTAAGGTTTTCTCTAGCTTACAGTATCAAACTATGATAATTAA
455 TCCTAATTAAACTAAGGATATATTAAGGTTTTCTCTAGCTTACAGTATCAAACTATGATAATTAA
1406362 AGAACCTAGAGGCATAAACCTAAAAATGTAGGCTCT-A-ATGAATCCTACTTGATTTTAACCAGT
520 AGAACCTAGAGGCATAAACCTAAAAATGTAGGCTCTAATATGAATCCTACTTGATTTTAACCAGT
1406425 TATTGAATCGAATAATTGAGATGGTCCCTTGTGCCTTTAGATAAGGGCCAACTCAAATTACACTC
585 TATTGAATCGAATAATTGAGATGGTCCCTTGTGCCTTTAGATAAGGGCCAACTCAAATTACACTC
1406490 TAAATTGAAGGGTCTAAATTGAAATCTAATCGAAAGTGGAGGCTCTAATTGTCCATCTAATCAAT
650 TAAATTGAAGGGTCTAAATTGAAATCTAATCGAAAGTGGAGGCTCTAATTGTCCATCTAATCAAT
1406555 TATGTCAAAAGGATAATCTAGTTAAAAGTTTAGGGATTAGAATGTGAGAAGCCAAGATTAAGGCT
715 TATGTCAAAAGGATAATCTAGTTAAAAGTTTAGGGATTAGAATGTGAGAAGCCAAGATTAAGGCT
1406620 CTAATTACTAACCCTAA
780 CTAATTACTAACCCTAA
* *
1406637 TTAACCTTACCAATCATTGAATCAAATAATCGAAATGAACCTTCGAGCATCTAAATGAGAGATCC
1 TTAACCTTACCAATCATTGAATCAAATAATCGAAATGAACATTCGAGCATCTAAATGAGAGATAC
1406702 AAATTGAATTATTCCCTAAATTAGACTAAAATGAAATCTAACTAATGTAGAGGTTTTAACATTAA
66 AAATTGAATTATTCCCTAAATTAGACTAAAATGAAATCTAACTAATGTAGAGGTTTTAACATTAA
1406767 TCTAAATTAATTTTAATCAATATTGCAATTCGAATAATTAAAGTGGAACCTCGAGCAAAAGCGGT
131 TCTAAATTAATTTTAATCAATATTGCAATTCGAATAATTAAAGTGGAACCTCGAGCAAAAGCGGT
1406832 GACCAAATTAAGAATTCTCCTAACTTAAAGATTAAATATGAAATTAGGCCTAATTTGGAGATAAT
196 GACCAAATTAAGAATTCTCCTAACTTAAAGATTAAATATGAAATTAGGCCTAATTTGGAGATAAT
*
1406897 CATTGTACCCAATAACCGGACATTGTCTTAATTTTGGAAATCATGATGCGGTCTTGAAAAAGATG
261 CATTGTACCCAATAACCGGACATTGTCTTAATTTTAGAAATCATGATGCGGTCTTGAAAAAGATG
1406962 TCGAACTATTTCGAGAATCACCAGTAGTCACCCCTTGAACATACTTGCGGGAGATATACTATCAA
326 TCGAACTATTTCGAGAATCACCAGTAGTCACCCCTTGAACATACTTGCGGGAGATATACTATCAA
*
1407027 ATCCCTAATAAATGAACAATACCTTAAATTTTGAAATAAAGAG-AATCAAATAATTTTTTATTAA
391 ATCCCTAATAAATGAACAATACCTTAAATTTTGAAATAAAG-GCAATCAAATAAATTTTTATTAA
1407091 TCCTAATTAAACTAAGGATATATTAAGGTTTTCTCTAGCTTACAGTATCAAACTATGATAATTAA
455 TCCTAATTAAACTAAGGATATATTAAGGTTTTCTCTAGCTTACAGTATCAAACTATGATAATTAA
1407156 AGAACCTAGAGGCATAAACCTAAAAATGTAGGCTCTAATATGAATCCTACTTGATTTTTAACCAG
520 AGAACCTAGAGGCATAAACCTAAAAATGTAGGCTCTAATATGAATCCTACTTGA-TTTTAACCAG
1407221 TTATTGAATCGAATAATTGAGATGGTCCCTTGTGCCTTTAGATAAGGGCCAACTCAAATTACACT
584 TTATTGAATCGAATAATTGAGATGGTCCCTTGTGCCTTTAGATAAGGGCCAACTCAAATTACACT
1407286 CTAAATTGAAGGGTCTAAATTGAAATCTAATCGAAAGTGGAGGCTCTAATTGTCCATCTAATCAA
649 CTAAATTGAAGGGTCTAAATTGAAATCTAATCGAAAGTGGAGGCTCTAATTGTCCATCTAATCAA
1407351 TTATGTCAAAAGGATAATCTAGTTAAAAGTTTAGGGATTAGAATGTGAGAAGCCAAGATTAAGGC
714 TTATGTCAAAAGGATAATCTAGTTAAAAGTTTAGGGATTAGAATGTGAGAAGCCAAGATTAAGGC
1407416 TCTAATTACTAACCCTAA
779 TCTAATTACTAACCCTAA
1407434 TTAACCTTACCAATCATTGAATCAAATAATCGAAATGAACATTCGAGCATCTAAATGAGAGATAC
1 TTAACCTTACCAATCATTGAATCAAATAATCGAAATGAACATTCGAGCATCTAAATGAGAGATAC
1407499 AAATTGAATTATTCCCTAAATTAGACTAAAATGAAATCTAACTAATGTAGAGGTTTTAACATTAA
66 AAATTGAATTATTCCCTAAATTAGACTAAAATGAAATCTAACTAATGTAGAGGTTTTAACATTAA
*
1407564 TCTAAATTAATTTTAATCAATATTACAATTCGAATAATTAAAGTGGAACCTCGAGCAAAAGCGGT
131 TCTAAATTAATTTTAATCAATATTGCAATTCGAATAATTAAAGTGGAACCTCGAGCAAAAGCGGT
*
1407629 GACCAAATTAAGAATTCTCCTAACTTGAAGATTAAATATGAAATTAGGCCTAATTTGGAGATAAT
196 GACCAAATTAAGAATTCTCCTAACTTAAAGATTAAATATGAAATTAGGCCTAATTTGGAGATAAT
* *
1407694 CATTGTACCCAATAACCAGACATTGTCTTAATTTTAGAAATCATGATGCGGTCTTGAAAAGGATG
261 CATTGTACCCAATAACCGGACATTGTCTTAATTTTAGAAATCATGATGCGGTCTTGAAAAAGATG
1407759 TCGAACTATTTCGAGAATCACCAGTAGTCACCCCTTGAACATACTTGCGGGAGATATACTATCAA
326 TCGAACTATTTCGAGAATCACCAGTAGTCACCCCTTGAACATACTTGCGGGAGATATACTATCAA
*
1407824 ATCCCTAATAAATGAATAATACCTTAAATTTTGAAATAAAGGCAATCAAATAAATTTTTATTAAT
391 ATCCCTAATAAATGAACAATACCTTAAATTTTGAAATAAAGGCAATCAAATAAATTTTTATTAAT
1407889 CCTAATTAAACTAAGGATATATTAAGGTTTTCTCTAGCTTACAGTATCAAACTATGATAATTAAA
456 CCTAATTAAACTAAGGATATATTAAGGTTTTCTCTAGCTTACAGTATCAAACTATGATAATTAAA
1407954 GAACCTAGAGGCATAAACCTAAAAATGTA
521 GAACCTAGAGGCATAAACCTAAAAATGTA
1407983 CTCGAATTAC
Statistics
Matches: 2092, Mismatches: 21, Indels: 32
0.98 0.01 0.01
Matches are distributed among these distances:
784 161 0.08
785 193 0.09
786 173 0.08
787 65 0.03
788 115 0.05
789 133 0.06
790 94 0.04
791 64 0.03
792 181 0.09
793 43 0.02
794 92 0.04
795 1 0.00
796 16 0.01
797 761 0.36
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.31
Consensus pattern (796 bp):
TTAACCTTACCAATCATTGAATCAAATAATCGAAATGAACATTCGAGCATCTAAATGAGAGATAC
AAATTGAATTATTCCCTAAATTAGACTAAAATGAAATCTAACTAATGTAGAGGTTTTAACATTAA
TCTAAATTAATTTTAATCAATATTGCAATTCGAATAATTAAAGTGGAACCTCGAGCAAAAGCGGT
GACCAAATTAAGAATTCTCCTAACTTAAAGATTAAATATGAAATTAGGCCTAATTTGGAGATAAT
CATTGTACCCAATAACCGGACATTGTCTTAATTTTAGAAATCATGATGCGGTCTTGAAAAAGATG
TCGAACTATTTCGAGAATCACCAGTAGTCACCCCTTGAACATACTTGCGGGAGATATACTATCAA
ATCCCTAATAAATGAACAATACCTTAAATTTTGAAATAAAGGCAATCAAATAAATTTTTATTAAT
CCTAATTAAACTAAGGATATATTAAGGTTTTCTCTAGCTTACAGTATCAAACTATGATAATTAAA
GAACCTAGAGGCATAAACCTAAAAATGTAGGCTCTAATATGAATCCTACTTGATTTTAACCAGTT
ATTGAATCGAATAATTGAGATGGTCCCTTGTGCCTTTAGATAAGGGCCAACTCAAATTACACTCT
AAATTGAAGGGTCTAAATTGAAATCTAATCGAAAGTGGAGGCTCTAATTGTCCATCTAATCAATT
ATGTCAAAAGGATAATCTAGTTAAAAGTTTAGGGATTAGAATGTGAGAAGCCAAGATTAAGGCTC
TAATTACTAACCCTAA
Found at i:1408883 original size:46 final size:46
Alignment explanation
Indices: 1408827--1408926 Score: 121
Period size: 46 Copynumber: 2.2 Consensus size: 46
1408817 TAGGGTTTTA
* * * *
1408827 TTTGGAGCTTAGTTTAGGGTTTTATTTAGGG-CTAATTTGTGTTTGG
1 TTTGGGGCTTAATTTAGGG-TTTATTTAGGGCCCAATTTATGTTTGG
* * *
1408873 TTTGGGGCTTAATTTAGGGTTTATTTTGGGCCCAGTTTATGTTTTG
1 TTTGGGGCTTAATTTAGGGTTTATTTAGGGCCCAATTTATGTTTGG
1408919 TTTGGGGC
1 TTTGGGGC
1408927 CTGGTTTGTA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
45 10 0.22
46 36 0.78
ACGTcount: A:0.13, C:0.07, G:0.31, T:0.49
Consensus pattern (46 bp):
TTTGGGGCTTAATTTAGGGTTTATTTAGGGCCCAATTTATGTTTGG
Found at i:1408900 original size:24 final size:24
Alignment explanation
Indices: 1408815--1408903 Score: 94
Period size: 23 Copynumber: 3.8 Consensus size: 24
1408805 TAGGGCATGG
* *
1408815 TTTAGGGTTTTATTTGGAGCTTAG
1 TTTAGGGTTTTATTTGGGGCTTAA
*
1408839 TTTAGGGTTTTATTTAGGGC-TAA
1 TTTAGGGTTTTATTTGGGGCTTAA
* **
1408862 TTT-GTGTTTGGTTTGGGGCTTAA
1 TTTAGGGTTTTATTTGGGGCTTAA
*
1408885 TTTAGGG-TTTATTTTGGGC
1 TTTAGGGTTTTATTTGGGGC
1408904 CCAGTTTATG
Statistics
Matches: 52, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
22 12 0.23
23 20 0.38
24 20 0.38
ACGTcount: A:0.15, C:0.04, G:0.30, T:0.51
Consensus pattern (24 bp):
TTTAGGGTTTTATTTGGGGCTTAA
Found at i:1409331 original size:139 final size:139
Alignment explanation
Indices: 1409079--1409794 Score: 917
Period size: 139 Copynumber: 5.2 Consensus size: 139
1409069 CTTTGAGCTC
* * * * ** *
1409079 TGAGTTCTTCTCATTATGAACTCTCCACTAGAAATGTTGATCCTTCAAGTGAGGCATCGCTGATT
1 TGAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGTGTCACTGATT
** * * **
1409144 CAACTCCATATACGATGAATTGAGCTAAGGTTGAACTAGTTCTTCTCATTGCGAACTTCTTCTCC
66 CAACTCCATATGTGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
1409209 CTCATCGGA
131 CTCATCGGA
* * * * *
1409218 TGAGTTCTTCTCATTATTAACTCTCTATTGGAAATGTTAATCCCTCTATTGACGTGTCACTGATT
1 TGAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGTGTCACTGATT
* * *
1409283 CAACTCCATATGCGATGAATC-AGGCTAAGGTTGAACATGTT-TTGCTCATTATGAAATTCTTCT
66 CAACTCCATATGTGATGAATCGA-GCTAAGGTTGAACAAGTTCTT-CTCATTATGAACTTCTTCT
1409346 CCCTCATCGGA
129 CCCTCATCGGA
* * * *
1409357 TGAGTTCTTCTCATTATGAACTCTCCACTT-GAAATGTTAATTCCTCGAGCGAGGTGTCACTAAT
1 TGAGTTCTTCTCATTATGAACTCTCCA-TTGGAAATGTTAATCCCTCAAGTGAGGTGTCACTGAT
* * * * * *
1409421 TTAACTTCGTATGTGATGAATCGAGCTAAGGTTGAATAAGTTCTTCTCATGATGAACTTATTCTC
65 TCAACTCCATATGTGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTC
*
1409486 CCTCATCAGA
130 CCTCATCGGA
* * * *
1409496 TGAGTTTTTCTCATTATGAACTCTCCTTTGGAAATGTTAATCCCTC-A---AGGCGTCGCTGATT
1 TGAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGTGTCACTGATT
1409557 CAACTCCATATGTGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
66 CAACTCCATATGTGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
*
1409622 CTCACCGGA
131 CTCATCGGA
* * * * * * * *
1409631 TGAGTTCTTATCATTATGAAATAC-CCAATGGAAATATTGATCCCTGAAGTGAGGTATCATTGAT
1 TGAGTTCTTCTCATTATGAACT-CTCCATTGGAAATGTTAATCCCTCAAGTGAGGTGTCACTGAT
* *
1409695 TCAACTCCTTATGTGATGAATCGAGCTAAGCTTGAACAAGTTCTTCTCATTATGAACTTCTTCTC
65 TCAACTCCATATGTGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTC
1409760 CCTCATCGGA
130 CCTCATCGGA
1409770 TGAGTTCTTCTCATTATGAACTCTC
1 TGAGTTCTTCTCATTATGAACTCTC
1409795 TACTGGTAAT
Statistics
Matches: 497, Mismatches: 68, Indels: 24
0.84 0.12 0.04
Matches are distributed among these distances:
135 113 0.23
136 2 0.00
138 7 0.01
139 370 0.74
140 5 0.01
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.36
Consensus pattern (139 bp):
TGAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGTGTCACTGATT
CAACTCCATATGTGATGAATCGAGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
CTCATCGGA
Found at i:1409710 original size:274 final size:277
Alignment explanation
Indices: 1409079--1409807 Score: 949
Period size: 274 Copynumber: 2.6 Consensus size: 277
1409069 CTTTGAGCTC
* * * *
1409079 TGAGTTCTTCTCATTATGAACTCTCCACTAGAAATGTTGATCCTTCAAGTGAGGCATCGCTGATT
1 TGAGTTCTTCTCATTATGAACTCTCCACTAGAAATGTTGATCCCTGAAGTGAGGTATCACTGATT
** * *
1409144 CAACTCCATATACGATGAATTGAGCTAAGGTTGAACT-AGTTCTTCTCATTG-CGAACTTCTTCT
66 CAACTCCATATGTGATGAATCGAGCTAAGGTTGAA-TAAGTTCTTCTCA-TGATGAACTTCTTCT
*
1409207 CCCTCATCGGATGAGTTCTTCTCATTATTAACTCT-CTATTGGAAATGTTAATCCCTCTATTGAC
129 CCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCTATTGGAAATGTTAATCCCTCTA-T-AC
* *
1409271 GTGTCACTGATTCAACTCCATATGCGATGAATCAGGCTAAGGTTGAACATGTTTTGCTCATTATG
192 GCGTCACTGATTCAACTCCATATGCGATGAATCAGGCTAAGGTTGAACAAGTTTTGCTCATTATG
*
1409336 AAATTCTTCTCCCTCATCGGA
257 AAATTCTTCTCCCTCACCGGA
* * * * * *
1409357 TGAGTTCTTCTCATTATGAACTCTCCACTTGAAATGTTAATTCCTCG-AGCGAGGTGTCACTAAT
1 TGAGTTCTTCTCATTATGAACTCTCCACTAGAAATGTTGATCCCT-GAAGTGAGGTATCACTGAT
* * * *
1409421 TTAACTTCGTATGTGATGAATCGAGCTAAGGTTGAATAAGTTCTTCTCATGATGAACTTATTCTC
65 TCAACTCCATATGTGATGAATCGAGCTAAGGTTGAATAAGTTCTTCTCATGATGAACTTCTTCTC
* * *
1409486 CCTCATCAGATGAGTTTTTCTCATTATGAACTCTCCT-TTGGAAATGTTAATCCCTC-A-AGGCG
130 CCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCTATTGGAAATGTTAATCCCTCTATACGCG
* *
1409548 TCGCTGATTCAACTCCATATGTGATGAATC-GAGCTAAGGTTGAACAAGTTCTT-CTCATTATGA
195 TCACTGATTCAACTCCATATGCGATGAATCAG-GCTAAGGTTGAACAAGTT-TTGCTCATTATGA
*
1409611 ACTTCTTCTCCCTCACCGGA
258 AATTCTTCTCCCTCACCGGA
* * * * * *
1409631 TGAGTTCTTATCATTATGAAATAC-CCAATGGAAATATTGATCCCTGAAGTGAGGTATCATTGAT
1 TGAGTTCTTCTCATTATGAACT-CTCCACTAGAAATGTTGATCCCTGAAGTGAGGTATCACTGAT
* * * *
1409695 TCAACTCCTTATGTGATGAATCGAGCTAAGCTTGAACAAGTTCTTCTCATTATGAACTTCTTCTC
65 TCAACTCCATATGTGATGAATCGAGCTAAGGTTGAATAAGTTCTTCTCATGATGAACTTCTTCTC
* *
1409760 CCTCATCGGATGAGTTCTTCTCATTATGAACTCT-CTACTGGTAATGTT
130 CCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCTATTGGAAATGTT
1409808 TATTGGTTTA
Statistics
Matches: 392, Mismatches: 50, Indels: 22
0.84 0.11 0.05
Matches are distributed among these distances:
273 4 0.01
274 224 0.57
275 3 0.01
277 4 0.01
278 155 0.40
279 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.36
Consensus pattern (277 bp):
TGAGTTCTTCTCATTATGAACTCTCCACTAGAAATGTTGATCCCTGAAGTGAGGTATCACTGATT
CAACTCCATATGTGATGAATCGAGCTAAGGTTGAATAAGTTCTTCTCATGATGAACTTCTTCTCC
CTCATCGGATGAGTTCTTCTCATTATGAACTCTCCTATTGGAAATGTTAATCCCTCTATACGCGT
CACTGATTCAACTCCATATGCGATGAATCAGGCTAAGGTTGAACAAGTTTTGCTCATTATGAAAT
TCTTCTCCCTCACCGGA
Found at i:1411605 original size:54 final size:54
Alignment explanation
Indices: 1411547--1411785 Score: 343
Period size: 54 Copynumber: 4.4 Consensus size: 54
1411537 CTATGTGTAA
* *
1411547 TATAGGCACTATGTGTGCAACCCACGAAATTCATTATATGTTGATGAACAACCG
1 TATAGGCACTATGTGTGCAACCCACAAAATTCATCATATGTTGATGAACAACCG
* * *
1411601 TATAGGCACTATGTGTGCAACTCACAAAATTGATCATATGTTGATGAACAACCA
1 TATAGGCACTATGTGTGCAACCCACAAAATTCATCATATGTTGATGAACAACCG
* * * *
1411655 TATAGGCACTATATGTGCAACCCATAAAATTAATCATATGTTGATAAACAACCG
1 TATAGGCACTATGTGTGCAACCCACAAAATTCATCATATGTTGATGAACAACCG
* * ** * *
1411709 TATAGGTACTATGTGTACAACCTTCAGAATTCATCATATGTTGATGAATAACCG
1 TATAGGCACTATGTGTGCAACCCACAAAATTCATCATATGTTGATGAACAACCG
1411763 TATAGGCACTATGTGTGCAACCC
1 TATAGGCACTATGTGTGCAACCC
1411786 TGTTGAGTTA
Statistics
Matches: 161, Mismatches: 24, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 161 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (54 bp):
TATAGGCACTATGTGTGCAACCCACAAAATTCATCATATGTTGATGAACAACCG
Found at i:1412514 original size:20 final size:21
Alignment explanation
Indices: 1412485--1412538 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 21
1412475 CATTATACAA
1412485 GGGGGAATCGGTACCCCC-TG
1 GGGGGAATCGGTACCCCCTTG
*
1412505 GGGTGAATCGGTACCCCCTTGG
1 GGGGGAATCGGTACCCCCTT-G
1412527 GGGGGAATCGGT
1 GGGGGAATCGGT
1412539 TCCCTCTGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 17 0.57
21 1 0.03
22 12 0.40
ACGTcount: A:0.15, C:0.24, G:0.43, T:0.19
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCCTTG
Found at i:1414647 original size:20 final size:20
Alignment explanation
Indices: 1414610--1414648 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1414600 AGATTGAGTG
* * *
1414610 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
1414630 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
1414649 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:1414856 original size:23 final size:21
Alignment explanation
Indices: 1414826--1414883 Score: 75
Period size: 23 Copynumber: 2.8 Consensus size: 21
1414816 TTCCCATGTG
1414826 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCC-TC-AA
1414849 GGGGGAATCGGTT-CCCTCAA
1 GGGGGAATCGGTTCCCCTCAA
*
1414869 GGGGG-ATCGATTCCC
1 GGGGGAATCGGTTCCC
1414884 TCTGTACCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
19 6 0.18
20 9 0.27
21 2 0.06
22 3 0.09
23 13 0.39
ACGTcount: A:0.19, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCCTCAA
Found at i:1420994 original size:54 final size:54
Alignment explanation
Indices: 1420934--1421684 Score: 1036
Period size: 54 Copynumber: 13.9 Consensus size: 54
1420924 GTTTTCAACA
* * * * * * *
1420934 AACCCACAAAATTCATCATATGTTTAAGAACAACCGTAAAGACGCAATGTGTGC
1 AACCCACGAAATTCATCATATGTTGATGAACAACCGTATAGGCACTATGTGTGC
*
1420988 CACCCACGAAATTCATCATATGTTGATGAACAACCGTATAGGCACTATGTGTGC
1 AACCCACGAAATTCATCATATGTTGATGAACAACCGTATAGGCACTATGTGTGC
**
1421042 AACCCACGAAATTCATCATATGTTTTTGAACAACCGTATAGGCACTATGTGTGC
1 AACCCACGAAATTCATCATATGTTGATGAACAACCGTATAGGCACTATGTGTGC
*
1421096 AACCGACGAAATTCATCATATGTTGATGAACAACCGTATAGGCACTATGTGTGC
1 AACCCACGAAATTCATCATATGTTGATGAACAACCGTATAGGCACTATGTGTGC
* * * *
1421150 AACCCACGTAATTAATCATATGTTGATGAACAACCATATAGGCACTATGTTTGC
1 AACCCACGAAATTCATCATATGTTGATGAACAACCGTATAGGCACTATGTGTGC
* * *
1421204 AATCCACGAAATTCATCATATGTTGATGAACAACCATATATGCACTATGTGTGC
1 AACCCACGAAATTCATCATATGTTGATGAACAACCGTATAGGCACTATGTGTGC
* * * *
1421258 AACCCATGGAATTCATCATATTTTGATGAACAACCATATAGGCACTATGTGTGC
1 AACCCACGAAATTCATCATATGTTGATGAACAACCGTATAGGCACTATGTGTGC
* *
1421312 CACCCACGAAATTCATCATATGTTGATGAACAACCATATAGGCACTATGTGTGC
1 AACCCACGAAATTCATCATATGTTGATGAACAACCGTATAGGCACTATGTGTGC
* *
1421366 AACCCACGGAATTCATCATATGTTGATGAACAACCGTATAGGCACTATGTGTGT
1 AACCCACGAAATTCATCATATGTTGATGAACAACCGTATAGGCACTATGTGTGC
* * * ** * * *
1421420 AACCCACGGAATTCATCATATGTTAATGAATAAAAATGTATAAGCATTATGTATGC
1 AACCCACGAAATTCATCATATGTTGATG-A-ACAACCGTATAGGCACTATGTGTGC
** *
1421476 AACCCATAAAATTCATCATATGTTGATGAACAACCGTATATGCACTATGTGTGC
1 AACCCACGAAATTCATCATATGTTGATGAACAACCGTATAGGCACTATGTGTGC
1421530 AACCCAC-AGAATTCATCATATGTTGATGAACAACCGTATAGGCACTATGTGTGC
1 AACCCACGA-AATTCATCATATGTTGATGAACAACCGTATAGGCACTATGTGTGC
* * * * *
1421584 AACCCACGTACTTCATCATATGTTGATGAACAACCATATAGGCACAACGTGTGC
1 AACCCACGAAATTCATCATATGTTGATGAACAACCGTATAGGCACTATGTGTGC
* * * * * *
1421638 AACCCAAGGAATGCATCATATGTTGATGAACGACCATATTGGCACTA
1 AACCCACGAAATTCATCATATGTTGATGAACAACCGTATAGGCACTA
1421685 CATGTTCATC
Statistics
Matches: 624, Mismatches: 69, Indels: 8
0.89 0.10 0.01
Matches are distributed among these distances:
53 1 0.00
54 579 0.93
55 2 0.00
56 42 0.07
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (54 bp):
AACCCACGAAATTCATCATATGTTGATGAACAACCGTATAGGCACTATGTGTGC
Found at i:1421144 original size:27 final size:27
Alignment explanation
Indices: 1421114--1421200 Score: 74
Period size: 27 Copynumber: 3.2 Consensus size: 27
1421104 AAATTCATCA
1421114 TATGTTGATGAACAACCGTATAGGCAC
1 TATGTTGATGAACAACCGTATAGGCAC
* **
1421141 TATG-TG-TGCAAC-CCACGTAATTAATCA-
1 TATGTTGATG-AACAAC-CGT-A-TAGGCAC
*
1421168 TATGTTGATGAACAACCATATAGGCAC
1 TATGTTGATGAACAACCGTATAGGCAC
1421195 TATGTT
1 TATGTT
1421201 TGCAATCCAC
Statistics
Matches: 45, Mismatches: 7, Indels: 16
0.66 0.10 0.24
Matches are distributed among these distances:
25 3 0.07
26 12 0.27
27 16 0.36
28 11 0.24
29 3 0.07
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (27 bp):
TATGTTGATGAACAACCGTATAGGCAC
Found at i:1421524 original size:27 final size:27
Alignment explanation
Indices: 1421494--1421579 Score: 72
Period size: 27 Copynumber: 3.2 Consensus size: 27
1421484 AAATTCATCA
1421494 TATGTTGATGAACAACCGTATATGCAC
1 TATGTTGATGAACAACCGTATATGCAC
* * *
1421521 TATG-TG-TGCAACCCACAG-A-ATTCATC
1 TATGTTGATG-AA-CAACCGTATATGCA-C
*
1421547 ATATGTTGATGAACAACCGTATAGGCAC
1 -TATGTTGATGAACAACCGTATATGCAC
1421575 TATGT
1 TATGT
1421580 GTGCAACCCA
Statistics
Matches: 44, Mismatches: 7, Indels: 16
0.66 0.10 0.24
Matches are distributed among these distances:
25 6 0.14
26 6 0.14
27 21 0.48
28 6 0.14
29 5 0.11
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.29
Consensus pattern (27 bp):
TATGTTGATGAACAACCGTATATGCAC
Found at i:1422440 original size:18 final size:18
Alignment explanation
Indices: 1422414--1422451 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1422404 TTGGAAATGG
1422414 TTGCAAGAGCAGTCTTCA
1 TTGCAAGAGCAGTCTTCA
* *
1422432 TTGCTAGAGTAGTCTTCA
1 TTGCAAGAGCAGTCTTCA
1422450 TT
1 TT
1422452 CTTTTCTTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (18 bp):
TTGCAAGAGCAGTCTTCA
Found at i:1424621 original size:29 final size:28
Alignment explanation
Indices: 1424577--1424646 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
1424567 ACTTGGGAAA
1424577 GTAATGTGTTTCAGGTTAATTTTGAGGAG
1 GTAATGTGTTTCAGGTTAA-TTTGAGGAG
* *
1424606 GTAATGTGTTTTAGGTTAATTTGGGGAG
1 GTAATGTGTTTCAGGTTAATTTGAGGAG
*
1424634 GTAATATGTTTCA
1 GTAATGTGTTTCA
1424647 TTTTGGCTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 19 0.51
29 18 0.49
ACGTcount: A:0.24, C:0.03, G:0.30, T:0.43
Consensus pattern (28 bp):
GTAATGTGTTTCAGGTTAATTTGAGGAG
Found at i:1424637 original size:28 final size:28
Alignment explanation
Indices: 1424559--1424644 Score: 100
Period size: 28 Copynumber: 3.0 Consensus size: 28
1424549 GATATAAGGC
* * * *
1424559 TTAGGATAACTTGGGAAAGTAATGTGTT
1 TTAGGTTAATTTGGGGAGGTAATGTGTT
* *
1424587 TCAGGTTAATTTTGAGGAGGTAATGTGTT
1 TTAGGTTAA-TTTGGGGAGGTAATGTGTT
*
1424616 TTAGGTTAATTTGGGGAGGTAATATGTT
1 TTAGGTTAATTTGGGGAGGTAATGTGTT
1424644 T
1 T
1424645 CATTTTGGCT
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
28 25 0.52
29 23 0.48
ACGTcount: A:0.27, C:0.02, G:0.30, T:0.41
Consensus pattern (28 bp):
TTAGGTTAATTTGGGGAGGTAATGTGTT
Found at i:1425331 original size:21 final size:20
Alignment explanation
Indices: 1425304--1425380 Score: 93
Period size: 21 Copynumber: 3.8 Consensus size: 20
1425294 TTTTCTTTAT
1425304 TTTTTTTCTCTCTTTTTTGC
1 TTTTTTTCTCTCTTTTTTGC
*
1425324 TTTATTTTCTCTCTATTTTGC
1 TTT-TTTTCTCTCTTTTTTGC
* *
1425345 TTTCTTTTCTATCTCTTCTT-C
1 TTT-TTTTCTCTCT-TTTTTGC
1425366 TTTTTTTCTCTCTTT
1 TTTTTTTCTCTCTTT
1425381 CTCTTTTTTG
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.04
20 12 0.24
21 32 0.65
22 3 0.06
ACGTcount: A:0.04, C:0.22, G:0.03, T:0.71
Consensus pattern (20 bp):
TTTTTTTCTCTCTTTTTTGC
Found at i:1425385 original size:21 final size:19
Alignment explanation
Indices: 1425304--1425389 Score: 84
Period size: 21 Copynumber: 4.3 Consensus size: 19
1425294 TTTTCTTTAT
1425304 TTTTTTTCTCTCTTTTTTGC
1 TTTTTTTCTCTCTTTTTT-C
*
1425324 TTTATTTTCTCTCTATTTTGC
1 TTT-TTTTCTCTCT-TTTTTC
* *
1425345 TTTCTTTTCTATCTCTTCTTC
1 TTT-TTTTCTCTCT-TTTTTC
*
1425366 TTTTTTTCTCTC-TTTCTC
1 TTTTTTTCTCTCTTTTTTC
1425384 TTTTTT
1 TTTTTT
1425390 GCCATATCTT
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
18 10 0.18
20 11 0.20
21 30 0.55
22 4 0.07
ACGTcount: A:0.03, C:0.22, G:0.02, T:0.72
Consensus pattern (19 bp):
TTTTTTTCTCTCTTTTTTC
Found at i:1430296 original size:35 final size:35
Alignment explanation
Indices: 1430250--1430319 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
1430240 CAAAATGCAC
1430250 AGTAACAAAGGTAAGCAAAATGATGCCAGTTTGGG
1 AGTAACAAAGGTAAGCAAAATGATGCCAGTTTGGG
* *
1430285 AGTAATAAAGGTAAGCAAAATGATGCCATTTTGGG
1 AGTAACAAAGGTAAGCAAAATGATGCCAGTTTGGG
1430320 GGTGCTCGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.40, C:0.10, G:0.27, T:0.23
Consensus pattern (35 bp):
AGTAACAAAGGTAAGCAAAATGATGCCAGTTTGGG
Found at i:1431224 original size:22 final size:22
Alignment explanation
Indices: 1431194--1431236 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1431184 GCTCCAATTG
1431194 GGCCCAGTTCGGGTTTGGTTTT
1 GGCCCAGTTCGGGTTTGGTTTT
* * *
1431216 GGCCTAGTTTGGGTTTTGTTT
1 GGCCCAGTTCGGGTTTGGTTT
1431237 AGGGTTTGGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.05, C:0.14, G:0.35, T:0.47
Consensus pattern (22 bp):
GGCCCAGTTCGGGTTTGGTTTT
Found at i:1431243 original size:12 final size:12
Alignment explanation
Indices: 1431222--1431311 Score: 60
Period size: 12 Copynumber: 7.6 Consensus size: 12
1431212 TTTTGGCCTA
*
1431222 GTTT-GGGTTTT
1 GTTTAGGGTTTG
1431233 GTTTAGGGTTTG
1 GTTTAGGGTTTG
1431245 GTTTAGGAGTTT-
1 GTTTAGG-GTTTG
* *
1431257 CTTT-GGGATATG
1 GTTTAGGG-TTTG
* *
1431269 GTTTAGAGTTTT
1 GTTTAGGGTTTG
* ** *
1431281 GTTTGGGGCCTA
1 GTTTAGGGTTTG
1431293 GTTTAGGGTTTG
1 GTTTAGGGTTTG
1431305 GTTTAGG
1 GTTTAGG
1431312 CTTGGGTTGT
Statistics
Matches: 58, Mismatches: 16, Indels: 9
0.70 0.19 0.11
Matches are distributed among these distances:
10 1 0.02
11 8 0.14
12 43 0.74
13 6 0.10
ACGTcount: A:0.11, C:0.03, G:0.37, T:0.49
Consensus pattern (12 bp):
GTTTAGGGTTTG
Found at i:1431285 original size:24 final size:24
Alignment explanation
Indices: 1431228--1431287 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
1431218 CCTAGTTTGG
*
1431228 GTTTTGTTTAGGGTTTGGTTTAGGA
1 GTTTTGTTT-GGGTATGGTTTAGGA
*
1431253 G-TTTCTTTGGGATATGGTTTA-GA
1 GTTTTGTTTGGG-TATGGTTTAGGA
1431276 GTTTTGTTTGGG
1 GTTTTGTTTGGG
1431288 GCCTAGTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 6 0.20
24 23 0.77
25 1 0.03
ACGTcount: A:0.12, C:0.02, G:0.35, T:0.52
Consensus pattern (24 bp):
GTTTTGTTTGGGTATGGTTTAGGA
Found at i:1435344 original size:22 final size:22
Alignment explanation
Indices: 1435306--1435351 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
1435296 ACTAGTTATT
**
1435306 ATATATATGATTTTTATCATGA
1 ATATATATGATGCTTATCATGA
*
1435328 ATATATATGATGCTTATTATGA
1 ATATATATGATGCTTATCATGA
1435350 AT
1 AT
1435352 GTTACTTCGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.48
Consensus pattern (22 bp):
ATATATATGATGCTTATCATGA
Found at i:1437708 original size:42 final size:42
Alignment explanation
Indices: 1437654--1437744 Score: 155
Period size: 42 Copynumber: 2.2 Consensus size: 42
1437644 TAGCCTTAGC
*
1437654 AACTTTTTTGTTTACTATTGCATATTTTTCTTGTCAAGATAG
1 AACTTTTTTGTTTACTATTGAATATTTTTCTTGTCAAGATAG
* *
1437696 GACTTTTTTGTTTACTATTGAATATTTTTCTTGTCGAGATAG
1 AACTTTTTTGTTTACTATTGAATATTTTTCTTGTCAAGATAG
1437738 AACTTTT
1 AACTTTT
1437745 CTGCGAGCTG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.23, C:0.11, G:0.13, T:0.53
Consensus pattern (42 bp):
AACTTTTTTGTTTACTATTGAATATTTTTCTTGTCAAGATAG
Found at i:1446088 original size:20 final size:20
Alignment explanation
Indices: 1446032--1446079 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1446022 GATGAACAGT
*
1446032 GGGGAATCGATTCCCTGTAG
1 GGGGAATCGATTCCCTCTAG
1446052 GGGGAATCGATTCCCTCTAG
1 GGGGAATCGATTCCCTCTAG
1446072 GGGGAATC
1 GGGGAATC
1446080 AATTACCTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.21, C:0.21, G:0.35, T:0.23
Consensus pattern (20 bp):
GGGGAATCGATTCCCTCTAG
Found at i:1448523 original size:13 final size:13
Alignment explanation
Indices: 1448505--1448532 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1448495 TTACATCATC
1448505 TTAATCGCAACCA
1 TTAATCGCAACCA
1448518 TTAATCGCAACCA
1 TTAATCGCAACCA
1448531 TT
1 TT
1448533 GCTGATATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (13 bp):
TTAATCGCAACCA
Found at i:1450067 original size:20 final size:20
Alignment explanation
Indices: 1450023--1450072 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1450013 AGATTTTTTT
1450023 ATGAATAGTGAACAGTATCCG
1 ATGAATAGTGAACAGTA-CCG
1450044 -TGAATAGTGAACAGTGA-CG
1 ATGAATAGTGAACAGT-ACCG
*
1450063 ATGAACAGTG
1 ATGAATAGTG
1450073 GGGGAATCGG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.08
20 23 0.88
21 1 0.04
ACGTcount: A:0.38, C:0.12, G:0.28, T:0.22
Consensus pattern (20 bp):
ATGAATAGTGAACAGTACCG
Found at i:1450593 original size:45 final size:44
Alignment explanation
Indices: 1450544--1450650 Score: 133
Period size: 45 Copynumber: 2.4 Consensus size: 44
1450534 ATAAAATCTT
* *
1450544 TTACCATTTATCCCATAAGCTCATAAGATTATTTTACCAAAATAC
1 TTACCATTT-TACCATAAGCTCATAAGATTATTTTACCAAAACAC
* * *
1450589 TTACCATTTGTACCATAAGCTCGTAAGCTTATTTTACCAATACAC
1 TTACCATTT-TACCATAAGCTCATAAGATTATTTTACCAAAACAC
* *
1450634 TTGCCATTTTTCCATAA
1 TTACCATTTTACCATAA
1450651 CCACATACCA
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
44 7 0.13
45 47 0.87
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (44 bp):
TTACCATTTTACCATAAGCTCATAAGATTATTTTACCAAAACAC
Found at i:1452444 original size:23 final size:23
Alignment explanation
Indices: 1452401--1452444 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1452391 TCAATCCAAT
* **
1452401 ATGAATTTCCATTTTTGCCATTA
1 ATGAATTTCCATATTCACCATTA
1452424 ATGAATTTCCATATTCACCAT
1 ATGAATTTCCATATTCACCAT
1452445 AAAACCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (23 bp):
ATGAATTTCCATATTCACCATTA
Found at i:1456338 original size:15 final size:15
Alignment explanation
Indices: 1456278--1456357 Score: 50
Period size: 13 Copynumber: 5.8 Consensus size: 15
1456268 ATTATTATTA
1456278 TATATATATATAATAT
1 TATATATATATAAT-T
* *
1456294 TA-ATAAATTTAATT
1 TATATATATATAATT
* *
1456308 TA-A-AT-TAAAATA
1 TATATATATATAATT
1456320 TATATATA-AT-ATT
1 TATATATATATAATT
1456333 TATATAT-T-TAATT
1 TATATATATATAATT
*
1456346 TAAATATATATA
1 TATATATATATA
1456358 CTTGGCCCGA
Statistics
Matches: 48, Mismatches: 9, Indels: 15
0.67 0.12 0.21
Matches are distributed among these distances:
12 7 0.15
13 20 0.42
14 8 0.17
15 11 0.23
16 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TATATATATATAATT
Found at i:1462092 original size:20 final size:20
Alignment explanation
Indices: 1462079--1462234 Score: 142
Period size: 20 Copynumber: 7.8 Consensus size: 20
1462069 GTAACACATA
*
1462079 AGTCAAATTCGTAACGCGAT
1 AGTCAAATTCGCAACGCGAT
* * *
1462099 AGTCAAATTCGCAACACAAA
1 AGTCAAATTCGCAACGCGAT
1462119 AGAT-AAATTCGCAACGCGAT
1 AG-TCAAATTCGCAACGCGAT
1462139 AGTCAAATTCGCAACGCGAATT
1 AGTCAAATTCGCAACGCG-A-T
* * *
1462161 TGT-AAA-TCGTAACAC-AT
1 AGTCAAATTCGCAACGCGAT
*
1462178 AAGTCAAATTTGCAACGCGAT
1 -AGTCAAATTCGCAACGCGAT
1462199 AGTCAAATTCGCAACGCGGA-
1 AGTCAAATTCGCAACGC-GAT
*
1462219 ATTTCAAATTCGCAAC
1 A-GTCAAATTCGCAAC
1462235 TGAATTTCAA
Statistics
Matches: 110, Mismatches: 16, Indels: 19
0.76 0.11 0.13
Matches are distributed among these distances:
17 1 0.01
18 3 0.03
19 4 0.04
20 77 0.70
21 22 0.20
22 3 0.03
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (20 bp):
AGTCAAATTCGCAACGCGAT
Found at i:1462115 original size:40 final size:40
Alignment explanation
Indices: 1462046--1462234 Score: 133
Period size: 40 Copynumber: 4.7 Consensus size: 40
1462036 AGTTTCCAAT
* *
1462046 TTCGCAACGCGA-ATTTCTAAA-TCGTAACAC-ATAAGTCAAA
1 TTCGCAACGCGATA-GTC-AAATTCGCAACACGATAAGT-AAA
* *
1462086 TTCGTAACGCGATAGTCAAATTCGCAACAC-AAAAGATAAA
1 TTCGCAACGCGATAGTCAAATTCGCAACACGATAAG-TAAA
* **
1462126 TTCGCAACGCGATAGTCAAATTCGCAACGCGAATTTGTAAA
1 TTCGCAACGCGATAGTCAAATTCGCAACACG-ATAAGTAAA
* * * *
1462167 -TCGTAACAC-ATAAGTCAAATTTGCAACGCGAT-AGTCAAA
1 TTCGCAACGCGAT-AGTCAAATTCGCAACACGATAAGT-AAA
*
1462206 TTCGCAACGCGGA-ATTTCAAATTCGCAAC
1 TTCGCAACGC-GATA-GTCAAATTCGCAAC
1462235 TGAATTTCAA
Statistics
Matches: 121, Mismatches: 17, Indels: 21
0.76 0.11 0.13
Matches are distributed among these distances:
38 2 0.02
39 10 0.08
40 88 0.73
41 18 0.15
42 3 0.02
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.23
Consensus pattern (40 bp):
TTCGCAACGCGATAGTCAAATTCGCAACACGATAAGTAAA
Found at i:1462245 original size:100 final size:98
Alignment explanation
Indices: 1461983--1462253 Score: 287
Period size: 100 Copynumber: 2.7 Consensus size: 98
1461973 AAATGACCAA
* * * * * * * *
1461983 CAAATTTGCAACGCGAT-CTCAAATTCGTAACG-TGAACTCTAATTTCGCAACCCAGTTTCCAAT
1 CAAATTTGCAACGCGATAGTCAAATTCGCAACGCAGAAATC-AAATTCGCAA-CGAATTT-CAAA
1462046 TTCGCAACGCGAATTTCTAAATCGTAACACATAAGT
63 TTCGCAACGCGAATTTCTAAATCGTAACACATAAGT
* * * * * *
1462082 CAAATTCGTAACGCGATAGTCAAATTCGCAACACAAAAGAT-AAATTCGCAACGCGATAGTCAAA
1 CAAATTTGCAACGCGATAGTCAAATTCGCAACGCAGAA-ATCAAATTCGCAACG-AAT-TTCAAA
*
1462146 TTCGCAACGCGAATTTGTAAATCGTAACACATAAGT
63 TTCGCAACGCGAATTTCTAAATCGTAACACATAAGT
* *
1462182 CAAATTTGCAACGCGATAGTCAAATTCGCAACGCGGAATTTCAAATTCGCAACTGAATTTCAAAT
1 CAAATTTGCAACGCGATAGTCAAATTCGCAACGCAGAA-ATCAAATTCGCAAC-GAATTTCAAAT
*
1462247 TTGCAAC
64 TCGCAAC
1462254 TAGATTTTTG
Statistics
Matches: 140, Mismatches: 25, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
99 16 0.11
100 106 0.76
101 16 0.11
102 2 0.01
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (98 bp):
CAAATTTGCAACGCGATAGTCAAATTCGCAACGCAGAAATCAAATTCGCAACGAATTTCAAATTC
GCAACGCGAATTTCTAAATCGTAACACATAAGT
Found at i:1462253 original size:60 final size:60
Alignment explanation
Indices: 1462079--1462234 Score: 185
Period size: 60 Copynumber: 2.6 Consensus size: 60
1462069 GTAACACATA
* * * *
1462079 AGTCAAATTCGTAACGCG-A-TAGTCAAATTCGCAACACAAAAGAT-AAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCGAATTTG-CAAA-TCGCAACACATAAG-TCAAATTTGCAACGCGAT
* *
1462139 AGTCAAATTCGCAACGCGAATTTGTAAATCGTAACACATAAGTCAAATTTGCAACGCGAT
1 AGTCAAATTCGCAACGCGAATTTGCAAATCGCAACACATAAGTCAAATTTGCAACGCGAT
1462199 AGTCAAATTCGCAACGCGGAATTT-CAAATTCGCAAC
1 AGTCAAATTCGCAACGC-GAATTTGCAAA-TCGCAAC
1462235 TGAATTTCAA
Statistics
Matches: 83, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
59 1 0.01
60 64 0.77
61 16 0.19
62 2 0.02
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (60 bp):
AGTCAAATTCGCAACGCGAATTTGCAAATCGCAACACATAAGTCAAATTTGCAACGCGAT
Found at i:1462272 original size:20 final size:19
Alignment explanation
Indices: 1462201--1462292 Score: 78
Period size: 19 Copynumber: 4.7 Consensus size: 19
1462191 AACGCGATAG
*
1462201 TCAAATTCGCAACGCGGAATT
1 TCAAATTCGCAA--CTGAATT
1462222 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
* *
1462241 TCAAATTTGCAACTAGATTT
1 TCAAATTCGCAACT-GAATT
** *
1462261 TTGAATTCGCAACACGAATT
1 TCAAATTCGCAAC-TGAATT
*
1462281 T-AATTTCGCAAC
1 TCAAATTCGCAAC
1462293 AGGTTTTAGT
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
19 28 0.47
20 19 0.32
21 12 0.20
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.32
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:1462468 original size:14 final size:15
Alignment explanation
Indices: 1462449--1462486 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1462439 TCCCCATCTC
1462449 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
1462463 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
1462479 TAATTTTT
1 TAATTTTT
1462487 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:1463430 original size:3 final size:3
Alignment explanation
Indices: 1463422--1463455 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1463412 ATATAACCCT
1463422 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1463456 TCCCCGAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1465247 original size:81 final size:81
Alignment explanation
Indices: 1465074--1465236 Score: 326
Period size: 81 Copynumber: 2.0 Consensus size: 81
1465064 TAAATGGGCT
1465074 TGTCGATCTAAATGCAAAGACGTGTAGTTGTAAGAAATGGCAAACATCTGGTTATCCGTGTGGCC
1 TGTCGATCTAAATGCAAAGACGTGTAGTTGTAAGAAATGGCAAACATCTGGTTATCCGTGTGGCC
1465139 ATGTTATAAAAGTTGC
66 ATGTTATAAAAGTTGC
1465155 TGTCGATCTAAATGCAAAGACGTGTAGTTGTAAGAAATGGCAAACATCTGGTTATCCGTGTGGCC
1 TGTCGATCTAAATGCAAAGACGTGTAGTTGTAAGAAATGGCAAACATCTGGTTATCCGTGTGGCC
1465220 ATGTTATAAAAGTTGC
66 ATGTTATAAAAGTTGC
1465236 T
1 T
1465237 CTTCATCTAA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.30
Consensus pattern (81 bp):
TGTCGATCTAAATGCAAAGACGTGTAGTTGTAAGAAATGGCAAACATCTGGTTATCCGTGTGGCC
ATGTTATAAAAGTTGC
Found at i:1465623 original size:18 final size:18
Alignment explanation
Indices: 1465600--1465635 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1465590 AAGCAAAAGG
*
1465600 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
1465618 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1465636 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1466126 original size:63 final size:62
Alignment explanation
Indices: 1466050--1466187 Score: 192
Period size: 63 Copynumber: 2.2 Consensus size: 62
1466040 AATTTAAAAC
*
1466050 AACAAATCAACTTTTACAACTCAATT-AAACAAGAAAAAAAATAA-TCTTATTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATTAAAACAAG-AAAAAAATAATTCTTATT--ACATC-AATT
1466113 A
62 A
* *
1466114 AA-AAATCAACTTTTACAAATCAATTAAAACAAGCAAAAAATAATTCTTATTTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAAACAAGAAAAAAATAATTCTTATTACATCAATTA
1466175 AACAAATCAACTT
1 AACAAATCAACTT
1466188 CAATGTAAAA
Statistics
Matches: 68, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
61 7 0.10
62 14 0.21
63 31 0.46
64 16 0.24
ACGTcount: A:0.54, C:0.17, G:0.01, T:0.28
Consensus pattern (62 bp):
AACAAATCAACTTTTACAAATCAATTAAAACAAGAAAAAAATAATTCTTATTACATCAATTA
Found at i:1466142 original size:25 final size:28
Alignment explanation
Indices: 1466085--1466142 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
1466075 TAAACAAGAA
*
1466085 AAAAAATAATCTTATTACACATCAAATT
1 AAAAAATAATCTTATTACAAATCAAATT
1466113 AAAAAATCAA-CTT-TTACAAATC-AATT
1 AAAAAAT-AATCTTATTACAAATCAAATT
1466139 AAAA
1 AAAA
1466143 CAAGCAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 8 0.29
27 8 0.29
28 10 0.36
29 2 0.07
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (28 bp):
AAAAAATAATCTTATTACAAATCAAATT
Found at i:1466218 original size:66 final size:62
Alignment explanation
Indices: 1466053--1466219 Score: 182
Period size: 63 Copynumber: 2.6 Consensus size: 62
1466043 TTAAAACAAC
*
1466053 AAATCAACTTTTACAACTCAATTAAACAAGA-AAAAAAATAATCTTATTACACATCAAATTAAA
1 AAATCAACTTTTACAAATCAATTAAACAA-ACAAAAAAATAATCTTATTA-ACATCAAATTAAA
* *
1466116 AAATCAACTTTTACAAATCAATTAAAACAAGC-AAAAAATAATTCTTATT-TCATC-AATTAAA
1 AAATCAACTTTTACAAATCAATT-AAACAAACAAAAAAATAA-TCTTATTAACATCAAATTAAA
1466177 CAAATCAACTTCAATGTA-AAATTCAATTAAACAAACAAAAAAA
1 -AAATCAACTT---T-TACAAA-TCAATTAAACAAACAAAAAAA
1466220 GTACCCAGAC
Statistics
Matches: 90, Mismatches: 4, Indels: 17
0.81 0.04 0.15
Matches are distributed among these distances:
61 7 0.08
62 14 0.16
63 31 0.34
64 13 0.14
65 11 0.12
66 14 0.16
ACGTcount: A:0.56, C:0.16, G:0.02, T:0.27
Consensus pattern (62 bp):
AAATCAACTTTTACAAATCAATTAAACAAACAAAAAAATAATCTTATTAACATCAAATTAAA
Found at i:1466312 original size:54 final size:54
Alignment explanation
Indices: 1466196--1466306 Score: 204
Period size: 56 Copynumber: 2.0 Consensus size: 54
1466186 TTCAATGTAA
1466196 AATTCAATTAAACAAACAAAAAAAGTACCCAGACTGTTGTTTATGCACAAATAC
1 AATTCAATTAAACAAACAAAAAAAGTACCCAGACTGTTGTTTATGCACAAATAC
1466250 AATTCAATTAAACAAACAAAAAAAGTGTACCCAGACTGTTGTTTATGCACAAATAC
1 AATTCAATTAAACAAACAAAAAAA--GTACCCAGACTGTTGTTTATGCACAAATAC
1466306 A
1 A
1466307 TCAATTTCAT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
54 24 0.44
56 31 0.56
ACGTcount: A:0.48, C:0.18, G:0.10, T:0.24
Consensus pattern (54 bp):
AATTCAATTAAACAAACAAAAAAAGTACCCAGACTGTTGTTTATGCACAAATAC
Found at i:1467643 original size:21 final size:21
Alignment explanation
Indices: 1467619--1467721 Score: 79
Period size: 21 Copynumber: 4.9 Consensus size: 21
1467609 GCGGGCGAGA
1467619 CCTCTTGAACGATGATAGGGG
1 CCTCTTGAACGATGATAGGGG
* **
1467640 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGATAGGGG
* * *
1467661 CTTCTTCG-ATGATGAGAGGGG
1 CCTCTT-GAACGATGATAGGGG
1467682 CCTCTTGAAC-A--ATAGGAGACG
1 CCTCTTGAACGATGATAGG-G--G
*
1467703 CCTCTTGAATGATGATAGG
1 CCTCTTGAACGATGATAGG
1467722 TGCATCGAGC
Statistics
Matches: 63, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
18 4 0.06
19 1 0.02
20 2 0.03
21 49 0.78
22 2 0.03
24 5 0.08
ACGTcount: A:0.23, C:0.18, G:0.34, T:0.24
Consensus pattern (21 bp):
CCTCTTGAACGATGATAGGGG
Found at i:1467715 original size:42 final size:42
Alignment explanation
Indices: 1467619--1467717 Score: 110
Period size: 42 Copynumber: 2.4 Consensus size: 42
1467609 GCGGGCGAGA
* * ** * **
1467619 CCTCTTGAACGATGATAGGGGCCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAATGATGAGAGGGGCCTCTTGAACAATAGGAGACG
*
1467661 CTTCTTCG-ATGATGAGAGGGGCCTCTTGAACAATAGGAGACG
1 CCTCTT-GAATGATGAGAGGGGCCTCTTGAACAATAGGAGACG
1467703 CCTCTTGAATGATGA
1 CCTCTTGAATGATGA
1467718 TAGGTGCATC
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
41 1 0.02
42 44 0.96
43 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.24
Consensus pattern (42 bp):
CCTCTTGAATGATGAGAGGGGCCTCTTGAACAATAGGAGACG
Found at i:1470258 original size:22 final size:22
Alignment explanation
Indices: 1470228--1470278 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1470218 GATGGAGATT
1470228 GACGGATTTCACCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
* **
1470250 GATGGATTTCGTCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
1470272 GACGGAT
1 GACGGAT
1470279 GTCGCCGTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.22, C:0.14, G:0.43, T:0.22
Consensus pattern (22 bp):
GACGGATTTCACCGGAGATGGG
Found at i:1470411 original size:20 final size:20
Alignment explanation
Indices: 1470388--1470590 Score: 169
Period size: 20 Copynumber: 10.1 Consensus size: 20
1470378 TAATATTGTG
*
1470388 TTTCGCGTTGCGAAATTGAC
1 TTTCGCGTTGCGAATTTGAC
**
1470408 TTTCGTATTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
*
1470428 TATCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
**
1470448 TTTTTCTGTTGCGAATTTGAC
1 TTTCGC-GTTGCGAATTTGAC
*** *
1470469 TTTTTTGTTGCGAATTTGGC
1 TTTCGCGTTGCGAATTTGAC
* * *
1470489 TATCTCGTTGCGAATTTAAC
1 TTTCGCGTTGCGAATTTGAC
* *
1470509 -TTCTGTGTTACG-ATTT-AC
1 TTTC-GCGTTGCGAATTTGAC
* *
1470527 AAATTCACGTTGCGAATTTGAC
1 --TTTCGCGTTGCGAATTTGAC
* *
1470549 TTTTGTGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
*
1470569 TATCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
1470589 TT
1 TT
1470591 CTATGTTTCG
Statistics
Matches: 145, Mismatches: 31, Indels: 14
0.76 0.16 0.07
Matches are distributed among these distances:
18 2 0.01
19 6 0.04
20 109 0.75
21 26 0.18
22 2 0.01
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.43
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAC
Found at i:1470468 original size:61 final size:61
Alignment explanation
Indices: 1470394--1470510 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 61
1470384 TGTGTTTCGC
*
1470394 GTTGCGAAATTGACTTTCGTATTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTTCT
1 GTTGCGAAATTGACTTTCGTATTGCGAATTTGACTATCGCGTTGCGAATTTAACTTTTTCT
* ** * * *
1470455 GTTGCGAATTTGACTTTTTTGTTGCGAATTTGGCTATCTCGTTGCGAATTTAACTT
1 GTTGCGAAATTGACTTTCGTATTGCGAATTTGACTATCGCGTTGCGAATTTAACTT
1470511 CTGTGTTACG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.19, C:0.15, G:0.21, T:0.44
Consensus pattern (61 bp):
GTTGCGAAATTGACTTTCGTATTGCGAATTTGACTATCGCGTTGCGAATTTAACTTTTTCT
Done.