Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009458.1 Hibiscus syriacus cultivar Beakdansim tig00113719_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: 1407308
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 6
Found at i:1076280 original size:16 final size:16
Alignment explanation
Indices: 1076256--1076299 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
1076246 TCAGTTAGGT
*
1076256 TTAATTTCGGTTCGGG
1 TTAATTTCGGTTCGGA
* *
1076272 TTAATTTCGATTCTGA
1 TTAATTTCGGTTCGGA
*
1076288 TTGATTTCGGTT
1 TTAATTTCGGTT
1076300 TTGGTAAATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.16, C:0.11, G:0.23, T:0.50
Consensus pattern (16 bp):
TTAATTTCGGTTCGGA
Found at i:1076631 original size:20 final size:19
Alignment explanation
Indices: 1076602--1076649 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
1076592 AATTTGAGTA
* *
1076602 TTTAAATTTTTACTTTTATT
1 TTTAATTTTTTACTTTT-TG
*
1076622 TTTAATTTTTTAGTTTTTG
1 TTTAATTTTTTACTTTTTG
1076641 TTTAATTTT
1 TTTAATTTT
1076650 AGTACTACAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.73
Consensus pattern (19 bp):
TTTAATTTTTTACTTTTTG
Found at i:1082769 original size:14 final size:14
Alignment explanation
Indices: 1082750--1082776 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1082740 ATTTTTATCG
1082750 AATAAATAAAATAA
1 AATAAATAAAATAA
1082764 AATAAATAAAATA
1 AATAAATAAAATA
1082777 TTACAATATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AATAAATAAAATAA
Found at i:1101518 original size:21 final size:21
Alignment explanation
Indices: 1101474--1101518 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1101464 TTAAGCTTTA
**
1101474 AAAATTAAAAATTTAGGTACT
1 AAAATTAAAAATTTAAATACT
* *
1101495 AAAATTAATAATTTAAATATT
1 AAAATTAAAAATTTAAATACT
1101516 AAA
1 AAA
1101519 TTCGTAGTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (21 bp):
AAAATTAAAAATTTAAATACT
Found at i:1101829 original size:60 final size:59
Alignment explanation
Indices: 1101714--1101864 Score: 212
Period size: 60 Copynumber: 2.5 Consensus size: 59
1101704 AAAAAAAATG
* * *
1101714 AAGTCCCTCGACTATTAAAAGTTATATAAATGGTCCTTCGACTTAGGATACTGCTTTGTT
1 AAGTCCCTCGACTATTAAAAGTTATA-AAATGGTCCTACAACTTAGAATACTGCTTTGTT
**
1101774 AAGTCCCTCGACTATTAAAAGTTATAAAATGGTCCTACAACTATAGAATGTTGCTTTGTT
1 AAGTCCCTCGACTATTAAAAGTTATAAAATGGTCCTACAACT-TAGAATACTGCTTTGTT
* * *
1101834 AAGTCTCTTGGCTATTAAAAGTTATAAAATG
1 AAGTCCCTCGACTATTAAAAGTTATAAAATG
1101865 ATCACTCAAT
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
59 14 0.17
60 68 0.83
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (59 bp):
AAGTCCCTCGACTATTAAAAGTTATAAAATGGTCCTACAACTTAGAATACTGCTTTGTT
Found at i:1102087 original size:60 final size:60
Alignment explanation
Indices: 1101980--1102121 Score: 160
Period size: 60 Copynumber: 2.4 Consensus size: 60
1101970 TTGGAACATA
* * * * *
1101980 ATTA-ATAGTCGGATGATCATTTTGTAACTTTTAATAGTCGACGGACTTAACAAAACAAC
1 ATTATATAGTCGAAGGATCATTTTATAACTTTTAATAGTCAACAGACTTAACAAAACAAC
* ** *
1102039 ATTATATAGTCGAAGGATCATTTTATAACTTTTAATAGTCAATAGACTTAATGAAACAAT
1 ATTATATAGTCGAAGGATCATTTTATAACTTTTAATAGTCAACAGACTTAACAAAACAAC
* * * *
1102099 ATCATATATTCGAGGGACCATTT
1 ATTATATAGTCGAAGGATCATTT
1102122 ATGTACTTTA
Statistics
Matches: 69, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
59 4 0.06
60 65 0.94
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (60 bp):
ATTATATAGTCGAAGGATCATTTTATAACTTTTAATAGTCAACAGACTTAACAAAACAAC
Found at i:1102517 original size:39 final size:40
Alignment explanation
Indices: 1102469--1102544 Score: 111
Period size: 39 Copynumber: 1.9 Consensus size: 40
1102459 AATAATTTAT
*
1102469 TTTAGTTATAATTTAAATCT-TTATAATTCATATATAATAA
1 TTTAGTTATAATTTAAAT-TGGTATAATTCATATATAATAA
*
1102509 TTTA-TTATAGTTTAAATTGGTATAATTCATATATAA
1 TTTAGTTATAATTTAAATTGGTATAATTCATATATAA
1102545 GTATAAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
38 1 0.03
39 28 0.85
40 4 0.12
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (40 bp):
TTTAGTTATAATTTAAATTGGTATAATTCATATATAATAA
Found at i:1114171 original size:3 final size:3
Alignment explanation
Indices: 1114163--1114222 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
1114153 TGTGTATATG
1114163 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1114211 TAA TAA TAA TAA
1 TAA TAA TAA TAA
1114223 AGATAATGTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1120592 original size:59 final size:59
Alignment explanation
Indices: 1120496--1120608 Score: 147
Period size: 59 Copynumber: 1.9 Consensus size: 59
1120486 TTATCTCCTG
** * *
1120496 ATTATAGAATATTATTTTATTAAGTTCTTTTATTATTAAAAGTAATAAAATGATCATTA
1 ATTATAGAATATTATTTTATTAAGTTCTTCAACTATTAAAAATAATAAAATGATCATTA
* * *
1120555 ATTATAGAATGTTATTTTGTTAAG-TCATTCAACTATTAAAAATTATAAAATGAT
1 ATTATAGAATATTATTTTATTAAGTTC-TTCAACTATTAAAAATAATAAAATGAT
1120609 TACCCAACTA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
58 2 0.04
59 44 0.96
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.45
Consensus pattern (59 bp):
ATTATAGAATATTATTTTATTAAGTTCTTCAACTATTAAAAATAATAAAATGATCATTA
Found at i:1122508 original size:20 final size:20
Alignment explanation
Indices: 1122414--1122782 Score: 451
Period size: 20 Copynumber: 18.4 Consensus size: 20
1122404 GATTTTCCAT
* ** *
1122414 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1122434 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1122454 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1122474 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
1122494 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
1122514 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1122534 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1122554 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1122574 AA-CTGCAACGTGTATCCGTA
1 AATC-GCAACGCGTATCCGTA
1122594 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1122614 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1122634 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1122654 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
1122674 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1122694 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1122714 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1122734 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1122754 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1122774 AATCACAAC
1 AATCGCAAC
1122783 ACTTAAATTT
Statistics
Matches: 305, Mismatches: 34, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
19 4 0.01
20 297 0.97
21 4 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1123503 original size:24 final size:24
Alignment explanation
Indices: 1123464--1123510 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1123454 AAATTTGGTC
1123464 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1123488 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1123511 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1123702 original size:12 final size:12
Alignment explanation
Indices: 1123685--1123709 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1123675 ATATAATCCT
1123685 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1123697 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1123709 G
1 G
1123710 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1126010 original size:19 final size:19
Alignment explanation
Indices: 1125988--1126280 Score: 383
Period size: 19 Copynumber: 16.4 Consensus size: 19
1125978 CGGAAAATAC
*
1125988 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1126007 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1126021 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
1126041 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1126055 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1126074 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1126093 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
1126107 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
1126126 AATCGCAATGCGGAATGAA
1 AATCGCAATGCGAAATGAA
1126145 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1126164 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1126183 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1126202 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1126221 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
1126235 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1126254 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1126273 AATCGCAA
1 AATCGCAA
1126281 CGAGATAATC
Statistics
Matches: 243, Mismatches: 10, Indels: 42
0.82 0.03 0.14
Matches are distributed among these distances:
14 38 0.16
15 1 0.00
16 14 0.06
17 12 0.05
18 2 0.01
19 163 0.67
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1126103 original size:52 final size:55
Alignment explanation
Indices: 1126016--1126302 Score: 347
Period size: 52 Copynumber: 5.4 Consensus size: 55
1126006 AAATCCCAAC
*
1126016 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA-CG-A-GAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAA
1126069 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGACA-G--AATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGA-ATGAAAATCGCAATGCGAA
* *
1126121 ATTAAAATCGCAATGCGGAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
1126178 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
1126233 A-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
*
1126283 A-GATAATCGCAATGCGAAAT
1 ATGAAAATCGCAATGCGAAAT
1126303 TATAAACGCA
Statistics
Matches: 220, Mismatches: 4, Indels: 21
0.90 0.02 0.09
Matches are distributed among these distances:
50 2 0.01
52 126 0.57
53 16 0.07
54 6 0.03
55 7 0.03
57 63 0.29
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (55 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAA
Found at i:1126199 original size:128 final size:128
Alignment explanation
Indices: 1125988--1126302 Score: 453
Period size: 128 Copynumber: 2.6 Consensus size: 128
1125978 CGGAAAATAC
* *
1125988 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCA
* *
1126048 A--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAG
65 ATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAG
* *
1126107 AATCGCAATGCGAAATTAAAATCGCAATGCGGAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1126172 TGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAG
66 TGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAG
*
1126235 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GATAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1126295 TGCGAAAT
66 TGCGAAAT
1126303 TATAAACGCA
Statistics
Matches: 178, Mismatches: 8, Indels: 16
0.88 0.04 0.08
Matches are distributed among these distances:
119 24 0.13
121 1 0.01
123 34 0.19
124 17 0.10
125 2 0.01
126 2 0.01
127 1 0.01
128 97 0.54
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (128 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
TGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAG
Found at i:1126293 original size:180 final size:176
Alignment explanation
Indices: 1125988--1126317 Score: 538
Period size: 180 Copynumber: 1.9 Consensus size: 176
1125978 CGGAAAATAC
*
1125988 AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAG
1 AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAA
1126053 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGC
66 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGC
1126118 GAAATTA-AAATCGCAATGCGGAATGAAAATCGCAATGCGAAATGAA
131 GAAATTATAAA-CGCAATGCGGAATGAAAATCGCAATGCGAAATGAA
* *
1126164 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAAAATCGCA
* *
1126228 ACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGC
61 ACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGC
*
1126293 AATGCGAAATTATAAACGCATTGCG
126 AATGCGAAATTATAAACGCAATGCG
1126318 ATTTTCATTT
Statistics
Matches: 142, Mismatches: 6, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
176 25 0.18
178 1 0.01
180 97 0.68
181 19 0.13
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (176 bp):
AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAA
AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGC
GAAATTATAAACGCAATGCGGAATGAAAATCGCAATGCGAAATGAA
Found at i:1126399 original size:19 final size:19
Alignment explanation
Indices: 1126309--1126391 Score: 113
Period size: 20 Copynumber: 4.6 Consensus size: 19
1126299 AAATTATAAA
1126309 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1126328 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
1126348 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
1126364 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1126381 CGCATTGCGAT
1 CGCATTGCGAT
1126392 AGTCATTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
14 6 0.11
16 7 0.12
17 7 0.12
19 17 0.30
20 19 0.34
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:1126517 original size:14 final size:14
Alignment explanation
Indices: 1126498--1126534 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1126488 CATCAATTAC
1126498 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1126512 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1126526 ACAAATCAA
1 ACAAATCAA
1126535 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1128512 original size:14 final size:14
Alignment explanation
Indices: 1128493--1128549 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1128483 GCGAAATGAA
*
1128493 AATCGCAACGACAG
1 AATCGCAACGAAAG
1128507 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1128524 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1128540 AATCGCAACG
1 AATCGCAACG
1128550 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1128520 original size:33 final size:33
Alignment explanation
Indices: 1128474--1128566 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1128464 GCGAAACCAA
*
1128474 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1128507 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1128540 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1128567 TGCTATTTCT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1128531 original size:19 final size:19
Alignment explanation
Indices: 1128437--1128566 Score: 127
Period size: 19 Copynumber: 7.3 Consensus size: 19
1128427 TAGTTTACTT
* *
1128437 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1128457 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1128476 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1128495 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1128509 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1128528 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1128542 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1128561 TCGCAA
1 TCGCAA
1128567 TGCTATTTCT
Statistics
Matches: 93, Mismatches: 7, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.17
16 11 0.12
17 11 0.12
19 43 0.46
20 12 0.13
ACGTcount: A:0.47, C:0.24, G:0.18, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1128896 original size:93 final size:93
Alignment explanation
Indices: 1128605--1129076 Score: 912
Period size: 93 Copynumber: 5.1 Consensus size: 93
1128595 TTGAATGGAT
1128605 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1128670 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1128698 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1128762 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1128790 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1128855 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
1128883 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATATAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1128947 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1128975 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1129040 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1129068 AAATTTACT
1 AAATTTACT
1129077 AAGCAATCTA
Statistics
Matches: 374, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
92 183 0.49
93 191 0.51
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1128917 original size:185 final size:185
Alignment explanation
Indices: 1128605--1129076 Score: 926
Period size: 185 Copynumber: 2.6 Consensus size: 185
1128595 TTGAATGGAT
1128605 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1128670 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1128735 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1128790 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1128855 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
1128920 TATATTTCACAGTGTTAAAGAATATACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1128975 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1129040 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
1129077 AAGCAATCTA
Statistics
Matches: 285, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
185 285 1.00
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (185 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1130800 original size:14 final size:14
Alignment explanation
Indices: 1130781--1130870 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1130771 TTGAAATGAA
1130781 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1130795 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
1130812 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
1130828 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1130847 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1130861 AATCGCAACG
1 AATCGCAACG
1130871 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1130818 original size:33 final size:33
Alignment explanation
Indices: 1130773--1130887 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1130763 TCTTTTGGTT
1130773 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1130806 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1130839 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1130872 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1130888 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1130819 original size:19 final size:18
Alignment explanation
Indices: 1130780--1130892 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
1130770 GTTGAAATGA
1130780 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
1130795 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
1130812 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
1130828 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
1130845 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
1130861 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
1130878 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
1130893 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:1130923 original size:14 final size:14
Alignment explanation
Indices: 1130904--1130958 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1130894 TTTGGTTTCG
1130904 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1130918 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1130937 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1130951 CGTTGCGA
1 CGTTGCGA
1130959 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1130936 original size:33 final size:33
Alignment explanation
Indices: 1130888--1130958 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1130878 AAAATCGCAA
**
1130888 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1130921 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1130954 TGCGA
1 TGCGA
1130959 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1130966 original size:33 final size:33
Alignment explanation
Indices: 1130899--1130980 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
1130889 GCGATTTTGG
***
1130899 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1130932 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
1130965 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
1130981 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:1130985 original size:20 final size:20
Alignment explanation
Indices: 1130911--1130999 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
1130901 TCGCGTTGCG
1130911 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1130931 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
1130944 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
1130964 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1130984 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
1131000 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:1131121 original size:33 final size:33
Alignment explanation
Indices: 1131079--1131149 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1131069 AATACTAACT
*
1131079 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1131112 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1131145 TGAAA
1 TGAAA
1131150 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:1131382 original size:22 final size:22
Alignment explanation
Indices: 1131330--1131382 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
1131320 TGGTTGTGAG
*
1131330 GGATTTCGTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1131352 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1131374 GGATTTCTT
1 GGATTTCTT
1131383 TGCCGTAGAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.21, C:0.13, G:0.40, T:0.26
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1131555 original size:20 final size:20
Alignment explanation
Indices: 1131530--1131722 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
1131520 CTTTAAATAT
1131530 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1131550 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1131572 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1131591 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1131611 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1131631 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1131651 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1131671 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1131691 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1131711 CGCGTTGCGATT
1 CGCGTTGCGATT
1131723 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1131717 original size:60 final size:60
Alignment explanation
Indices: 1131530--1131722 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
1131520 CTTTAAATAT
**
1131530 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
1131591 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
1131651 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
1131711 CGCGTTGCGATT
1 CGCGTTGCGATT
1131723 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:1131803 original size:20 final size:20
Alignment explanation
Indices: 1131778--1131829 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1131768 AAGAATCGCG
*
1131778 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1131798 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1131818 TTGCGATTCTGG
1 TTGCGATTCTGG
1131830 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:1133918 original size:5 final size:5
Alignment explanation
Indices: 1133908--1133951 Score: 52
Period size: 5 Copynumber: 8.2 Consensus size: 5
1133898 TACGTTTAAA
*
1133908 TATTT TATTT TATTTT TAGTT TATTCT TATTCT TATTT TATTT T
1 TATTT TATTT TA-TTT TATTT TATT-T TATT-T TATTT TATTT T
1133952 TTCACTAACC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 19 0.54
6 16 0.46
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (5 bp):
TATTT
Found at i:1133930 original size:11 final size:11
Alignment explanation
Indices: 1133910--1133951 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
1133900 CGTTTAAATA
1133910 TTTTATTTTAT
1 TTTTATTTTAT
*
1133921 TTTTAGTTTAT
1 TTTTATTTTAT
*
1133932 TCTTATTCTTA-
1 TTTTATT-TTAT
1133943 TTTTATTTT
1 TTTTATTTT
1133952 TTCACTAACC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 2 0.08
11 21 0.81
12 3 0.12
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:1134021 original size:25 final size:25
Alignment explanation
Indices: 1133984--1134038 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
1133974 ATTTTATTCA
1133984 TTTTATTTATTTTCTTT-CTTTCTT
1 TTTTATTTATTTTCTTTACTTTCTT
* *
1134008 TCTTTA-TTATTTTTGTTTATTTTCTT
1 T-TTTATTTA-TTTTCTTTACTTTCTT
1134034 TTTTA
1 TTTTA
1134039 CTAACTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 15 0.58
26 7 0.27
ACGTcount: A:0.11, C:0.09, G:0.02, T:0.78
Consensus pattern (25 bp):
TTTTATTTATTTTCTTTACTTTCTT
Found at i:1137135 original size:16 final size:16
Alignment explanation
Indices: 1137109--1137154 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
1137099 AGATCCAATC
1137109 AAGAACAAAAAAG-AA
1 AAGAACAAAAAAGCAA
1137124 AAGAATCAAAAAAGCAA
1 AAGAA-CAAAAAAGCAA
1137141 AA-AA-AAAAAA-CAA
1 AAGAACAAAAAAGCAA
1137154 A
1 A
1137155 GAAAAAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
13 4 0.14
14 6 0.21
15 5 0.17
16 10 0.34
17 4 0.14
ACGTcount: A:0.80, C:0.09, G:0.09, T:0.02
Consensus pattern (16 bp):
AAGAACAAAAAAGCAA
Found at i:1137875 original size:23 final size:22
Alignment explanation
Indices: 1137833--1137875 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1137823 CCATCAATCT
* *
1137833 TTTGAGCATCCAATGCCAAACC
1 TTTGAGCATCAAATGACAAACC
1137855 TTTGAGCATCAAATGAACAAA
1 TTTGAGCATCAAATG-ACAAA
1137876 AATGCCAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.23
Consensus pattern (22 bp):
TTTGAGCATCAAATGACAAACC
Found at i:1139404 original size:209 final size:210
Alignment explanation
Indices: 1139039--1139569 Score: 859
Period size: 209 Copynumber: 2.5 Consensus size: 210
1139029 ATATCGTGCC
* *
1139039 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAATAAACAACTTCCC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
1139104 AATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACT
*
1139169 TCACGACGAAGGGACCGCTGGTTGTCAACAAAC-TTCCCAATTTCAGAGCCAATTTCAACTTCAC
131 TCACGAAGAAGGGACCGCTGGTTGTCAACAAACATTCCCAATTTCAGAGCCAATTTCAACTTCAC
1139233 AACGAAGGATATTAG
196 AACGAAGGATATTAG
*
1139248 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
1139313 AATTTCAGATCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAATGCAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACT
*
1139378 TCACGAAGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCAATTTCAACTTC
131 TCACGAAGAAGGGACCGCTGGTTGTCAACAAAC-A-TTCCCAATTTCAGAGCCAATTTCAACTTC
*
1139443 ACAGCGAAGGATATTAG
194 ACAACGAAGGATATTAG
* * * * *
1139460 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* * *
1139525 AGTTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGGACTC
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTC
1139570 GGAACAATGC
Statistics
Matches: 299, Mismatches: 19, Indels: 5
0.93 0.06 0.02
Matches are distributed among these distances:
209 155 0.52
211 1 0.00
212 143 0.48
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (210 bp):
ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACT
TCACGAAGAAGGGACCGCTGGTTGTCAACAAACATTCCCAATTTCAGAGCCAATTTCAACTTCAC
AACGAAGGATATTAG
Found at i:1139570 original size:106 final size:106
Alignment explanation
Indices: 1139039--1139569 Score: 836
Period size: 106 Copynumber: 5.0 Consensus size: 106
1139029 ATATCGTGCC
* * *
1139039 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAATAAACAACTTCCC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
*
1139104 AATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
1139145 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC---TTCCC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* *
1139207 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1139248 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
*
1139313 AATTTCAGATCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1139354 ACTCAAGACAATGCAAGTTCAACTTCACGAAGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* *
1139419 AATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
1139460 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* * *
1139525 AGTTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
1139566 ACTC
1 ACTC
1139570 GGAACAATGC
Statistics
Matches: 393, Mismatches: 28, Indels: 8
0.92 0.07 0.02
Matches are distributed among these distances:
103 99 0.25
105 1 0.00
106 293 0.75
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (106 bp):
ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:1141094 original size:5 final size:5
Alignment explanation
Indices: 1141084--1141127 Score: 52
Period size: 5 Copynumber: 8.2 Consensus size: 5
1141074 TACGTTTAAA
*
1141084 TATTT TATTT TATTTT TAGTT TATTCT TATTCT TATTT TATTT T
1 TATTT TATTT TA-TTT TATTT TATT-T TATT-T TATTT TATTT T
1141128 TTCACTAACC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 19 0.54
6 16 0.46
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (5 bp):
TATTT
Found at i:1141106 original size:11 final size:11
Alignment explanation
Indices: 1141086--1141127 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
1141076 CGTTTAAATA
1141086 TTTTATTTTAT
1 TTTTATTTTAT
*
1141097 TTTTAGTTTAT
1 TTTTATTTTAT
*
1141108 TCTTATTCTTA-
1 TTTTATT-TTAT
1141119 TTTTATTTT
1 TTTTATTTT
1141128 TTCACTAACC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 2 0.08
11 21 0.81
12 3 0.12
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:1141562 original size:198 final size:198
Alignment explanation
Indices: 1141224--1141621 Score: 796
Period size: 198 Copynumber: 2.0 Consensus size: 198
1141214 CTTTTAATTA
1141224 TCTCTGTTACTTATTTTATCTTAGAATTTTTTCCTCGTATTTATTTTTATTTTATCATCTAACCT
1 TCTCTGTTACTTATTTTATCTTAGAATTTTTTCCTCGTATTTATTTTTATTTTATCATCTAACCT
1141289 TTTTTGGCATTTTCAGTGGTAATTTCAATCGATCAAAGGTAATAATTCGAATCGAATATTTCAAG
66 TTTTTGGCATTTTCAGTGGTAATTTCAATCGATCAAAGGTAATAATTCGAATCGAATATTTCAAG
1141354 TTTTAATTTAAATTTCTAATTTTCGCAATTAAGACAACTGACAAATTAATTGGTACCGAAAGGGC
131 TTTTAATTTAAATTTCTAATTTTCGCAATTAAGACAACTGACAAATTAATTGGTACCGAAAGGGC
1141419 GGT
196 GGT
1141422 TCTCTGTTACTTATTTTATCTTAGAATTTTTTCCTCGTATTTATTTTTATTTTATCATCTAACCT
1 TCTCTGTTACTTATTTTATCTTAGAATTTTTTCCTCGTATTTATTTTTATTTTATCATCTAACCT
1141487 TTTTTGGCATTTTCAGTGGTAATTTCAATCGATCAAAGGTAATAATTCGAATCGAATATTTCAAG
66 TTTTTGGCATTTTCAGTGGTAATTTCAATCGATCAAAGGTAATAATTCGAATCGAATATTTCAAG
1141552 TTTTAATTTAAATTTCTAATTTTCGCAATTAAGACAACTGACAAATTAATTGGTACCGAAAGGGC
131 TTTTAATTTAAATTTCTAATTTTCGCAATTAAGACAACTGACAAATTAATTGGTACCGAAAGGGC
1141617 GGT
196 GGT
1141620 TC
1 TC
1141622 AAGGGTGCTA
Statistics
Matches: 200, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
198 200 1.00
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.44
Consensus pattern (198 bp):
TCTCTGTTACTTATTTTATCTTAGAATTTTTTCCTCGTATTTATTTTTATTTTATCATCTAACCT
TTTTTGGCATTTTCAGTGGTAATTTCAATCGATCAAAGGTAATAATTCGAATCGAATATTTCAAG
TTTTAATTTAAATTTCTAATTTTCGCAATTAAGACAACTGACAAATTAATTGGTACCGAAAGGGC
GGT
Found at i:1144265 original size:9 final size:9
Alignment explanation
Indices: 1144225--1144276 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
1144215 AATATTAGAT
1144225 AAAAAATATG
1 AAAAAATA-G
*
1144235 AAATAAATAT
1 AAA-AAATAG
* *
1144245 TAAAAAGA-
1 AAAAAATAG
1144253 AAAAAATAG
1 AAAAAATAG
1144262 AAAAAATAG
1 AAAAAATAG
1144271 AAAAAA
1 AAAAAA
1144277 AAACAATAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
8 6 0.17
9 19 0.54
10 5 0.14
11 5 0.14
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (9 bp):
AAAAAATAG
Found at i:1144275 original size:26 final size:28
Alignment explanation
Indices: 1144225--1144276 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
1144215 AATATTAGAT
**
1144225 AAAAAATATGAAATAAATATTAAAAAGA
1 AAAAAATATGAAATAAATAGAAAAAAGA
1144253 AAAAAATA-GAAA-AAATAGAAAAAA
1 AAAAAATATGAAATAAATAGAAAAAA
1144277 AAACAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 10 0.45
27 4 0.18
28 8 0.36
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (28 bp):
AAAAAATATGAAATAAATAGAAAAAAGA
Found at i:1146210 original size:106 final size:106
Alignment explanation
Indices: 1146082--1147076 Score: 1503
Period size: 106 Copynumber: 9.4 Consensus size: 106
1146072 GTATTGTTCC
* * * * *
1146082 GAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTGGAACTG-GTAAATTGTTTATTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AAGTTGTTTATTGACA
** * * * * * *
1146146 GTCAGCCGCCCCTTCGGT-GTGAAGTTGAGCTTGTGCTGTCTT
65 ACCAGCGGTCCCTTC-GTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1146188 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
* * *
1146253 CCAACGGTCCCTTTGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* ** * *
1146294 GAGTCGAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
* * * * * * *
1146359 TCAGCCGCCCCTTCG-CTGTGAAGTTGAGCTTGTGCTGTCTT
66 CCAGCGGTCCCTTCGTC-GTGAAGTTGAACTTGCGTTGTCTG
* *
1146400 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
*
1146465 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1146506 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
* *
1146571 CCAGCGGTCCCTTCGTCATGAAGTTGAACATGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1146612 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1146677 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1146718 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGATATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1146783 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1146824 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1146889 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1146930 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGATATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
*
1146995 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1147036 GAGTCCAATATCCTTCGCTGT-AAGTTGAAATAGACTCTGAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAA
1147077 TGAAATTCGA
Statistics
Matches: 817, Mismatches: 68, Indels: 9
0.91 0.08 0.01
Matches are distributed among these distances:
105 20 0.02
106 795 0.97
107 2 0.00
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1151054 original size:35 final size:36
Alignment explanation
Indices: 1150976--1151054 Score: 83
Period size: 35 Copynumber: 2.2 Consensus size: 36
1150966 GAAAAAAAAT
* *
1150976 AGAAAAAATAGAAAATACAATAAAATAATAAATTAA
1 AGAAAAAATAGAAAATACAATAAAATAACAAATCAA
* *
1151012 ATGAAAAATATA-ATAATA-AAT-GAATAACAAATCAA
1 A-GAAAAA-ATAGAAAATACAATAAAATAACAAATCAA
1151047 AGAAAAAA
1 AGAAAAAA
1151055 GTAAATTTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
33 1 0.03
34 6 0.16
35 12 0.32
36 4 0.11
37 11 0.30
38 3 0.08
ACGTcount: A:0.71, C:0.04, G:0.06, T:0.19
Consensus pattern (36 bp):
AGAAAAAATAGAAAATACAATAAAATAACAAATCAA
Found at i:1153763 original size:26 final size:28
Alignment explanation
Indices: 1153702--1153763 Score: 65
Period size: 31 Copynumber: 2.2 Consensus size: 28
1153692 GAGTATTGCT
* *
1153702 GAGCTCGACTCGACTCGAAAACTCTGAAAT
1 GAGCTCAACTCGACTCGAAAACTCTG--AC
1153732 GAAGCTCAACTCGACTCGAAAACTC-G-C
1 G-AGCTCAACTCGACTCGAAAACTCTGAC
1153759 GAGCT
1 GAGCT
1153764 TAAAATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
26 4 0.14
27 1 0.03
30 2 0.07
31 22 0.76
ACGTcount: A:0.32, C:0.29, G:0.21, T:0.18
Consensus pattern (28 bp):
GAGCTCAACTCGACTCGAAAACTCTGAC
Found at i:1154710 original size:59 final size:59
Alignment explanation
Indices: 1154566--1154701 Score: 159
Period size: 59 Copynumber: 2.3 Consensus size: 59
1154556 AACATAATGA
* * *
1154566 ATAGCCGAGAGACCATTTTATAAC-TCCTAATAGTTGAGGGACTCAACAAAGCAACATCCT
1 ATAGCCG-GAGACCATTTTATAACTTTC-AATAGTCGAGGGACTCAACAAAACAACATCCT
* * **
1154626 ATAGTCGGAGACCATTTTATAACTTTCAATAGTCGAGGGACTCAATAAAACATTATCCT
1 ATAGCCGGAGACCATTTTATAACTTTCAATAGTCGAGGGACTCAACAAAACAACATCCT
*
1154685 ATA-CCGGGGGACCATTT
1 ATAGCC-GGAGACCATTT
1154702 GTGTACTTTA
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
58 1 0.02
59 56 0.86
60 8 0.12
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (59 bp):
ATAGCCGGAGACCATTTTATAACTTTCAATAGTCGAGGGACTCAACAAAACAACATCCT
Found at i:1155440 original size:30 final size:31
Alignment explanation
Indices: 1155405--1155463 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
1155395 TCGTTACTTT
* *
1155405 TTTTA-GTATCGGTCGTTGTATTTTTTAAAC
1 TTTTAGGTATCGATCGTTATATTTTTTAAAC
* *
1155435 TTTTAGGTATCTATTGTTATATTTTTTAA
1 TTTTAGGTATCGATCGTTATATTTTTTAA
1155464 TTGTTTAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 5 0.21
31 19 0.79
ACGTcount: A:0.22, C:0.07, G:0.14, T:0.58
Consensus pattern (31 bp):
TTTTAGGTATCGATCGTTATATTTTTTAAAC
Found at i:1155940 original size:24 final size:24
Alignment explanation
Indices: 1155908--1155956 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
1155898 AACATATAAA
*
1155908 ACGAGTCGGGTCAGTTTGAATTGG
1 ACGAGTCGGGTCAATTTGAATTGG
1155932 ACGAGTCGGGTCAATTTGAATTGG
1 ACGAGTCGGGTCAATTTGAATTGG
1155956 A
1 A
1155957 TTTGAACCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.12, G:0.35, T:0.29
Consensus pattern (24 bp):
ACGAGTCGGGTCAATTTGAATTGG
Found at i:1156755 original size:2 final size:2
Alignment explanation
Indices: 1156748--1156879 Score: 264
Period size: 2 Copynumber: 66.0 Consensus size: 2
1156738 TTGATCATTA
1156748 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
1156790 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
1156832 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
1156874 AT AT AT
1 AT AT AT
1156880 TGTCAAATTA
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 130 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1159361 original size:23 final size:23
Alignment explanation
Indices: 1159335--1159384 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1159325 CAATATAATT
*
1159335 TGATGAATTATA-AATATATAAAG
1 TGATGAATAATATAATAT-TAAAG
* *
1159358 TGATTAATAATATAATATTAATG
1 TGATGAATAATATAATATTAAAG
1159381 TGAT
1 TGAT
1159385 ATATGTCACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (23 bp):
TGATGAATAATATAATATTAAAG
Found at i:1163411 original size:29 final size:29
Alignment explanation
Indices: 1163369--1163434 Score: 114
Period size: 29 Copynumber: 2.3 Consensus size: 29
1163359 AAACTATGGG
*
1163369 TTAGTGACCAAATTGTAAAATTTTAGAAT
1 TTAGTGACCAAATTATAAAATTTTAGAAT
*
1163398 TTAGTTACCAAATTATAAAATTTTAGAAT
1 TTAGTGACCAAATTATAAAATTTTAGAAT
1163427 TTAGTGAC
1 TTAGTGAC
1163435 TAAAGTAGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (29 bp):
TTAGTGACCAAATTATAAAATTTTAGAAT
Found at i:1164304 original size:29 final size:29
Alignment explanation
Indices: 1164262--1164338 Score: 109
Period size: 29 Copynumber: 2.7 Consensus size: 29
1164252 AAACTATGGG
* *
1164262 TTAGTGACCAAATTGTAAAATTTCATAAT
1 TTAGTGACCAAATTATAAAATTTCAGAAT
*
1164291 TTAGTGACCAAATTATAAAATTTTAGAAT
1 TTAGTGACCAAATTATAAAATTTCAGAAT
* *
1164320 TTAGTGACTAAAGTATAAA
1 TTAGTGACCAAATTATAAA
1164339 TAATTGAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (29 bp):
TTAGTGACCAAATTATAAAATTTCAGAAT
Found at i:1165220 original size:19 final size:20
Alignment explanation
Indices: 1165173--1165217 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
1165163 GGATGTATCA
*
1165173 ATACCCTATGGGGGGTACCG
1 ATACCCTATAGGGGGTACCG
1165193 ATACCCTATAGGGGGTACCG
1 ATACCCTATAGGGGGTACCG
1165213 ATACC
1 ATACC
1165218 TATTTTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.24, C:0.27, G:0.29, T:0.20
Consensus pattern (20 bp):
ATACCCTATAGGGGGTACCG
Found at i:1165761 original size:22 final size:22
Alignment explanation
Indices: 1165712--1165775 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
1165702 TGAGGGTTAT
* *
1165712 ATAGGTCATTCGGGACATATAC
1 ATAGGTCCTTCGGGACAAATAC
* * *
1165734 AGAGGTCCTTCGGGATAAATTC
1 ATAGGTCCTTCGGGACAAATAC
* *
1165756 ATAGGTCCTTCAGAACAAAT
1 ATAGGTCCTTCGGGACAAAT
1165776 TTCACATGCC
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.27
Consensus pattern (22 bp):
ATAGGTCCTTCGGGACAAATAC
Found at i:1167836 original size:50 final size:51
Alignment explanation
Indices: 1167712--1167956 Score: 289
Period size: 51 Copynumber: 4.8 Consensus size: 51
1167702 AGATGTACAT
* * * *
1167712 ACTTACATCGGTGTAAGTATATGTTAAGTGCTACACTTTTTTATTTTGTTT
1 ACTTACATCGGTGTAAGTATGTGTTAAGTACTACACTTTTTTATTTTATTC
* * *
1167763 ACTTACATCGTTGTAAGTATGTGTTAAATACTACATTTTTTTATTTTATTC
1 ACTTACATCGGTGTAAGTATGTGTTAAGTACTACACTTTTTTATTTTATTC
* *
1167814 ACTTA-AGTTGGTGT-AGTATGTGTTAAGTACTACACTTTTTTGTTTTATTC
1 ACTTACA-TCGGTGTAAGTATGTGTTAAGTACTACACTTTTTTATTTTATTC
* * * *
1167864 ACTTACACCGGTGTAAGTTTGTATTAAGTGA-TACACTTGTTTATTTTATTC
1 ACTTACATCGGTGTAAGTATGTGTTAAGT-ACTACACTTTTTTATTTTATTC
* * * * *
1167915 ACTTACACCGATGTAAATATGTGTTAAGTACTATATTTTTTT
1 ACTTACATCGGTGTAAGTATGTGTTAAGTACTACACTTTTTT
1167957 TGTAATAATA
Statistics
Matches: 164, Mismatches: 25, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
50 45 0.27
51 118 0.72
52 1 0.01
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (51 bp):
ACTTACATCGGTGTAAGTATGTGTTAAGTACTACACTTTTTTATTTTATTC
Found at i:1167954 original size:101 final size:102
Alignment explanation
Indices: 1167712--1167956 Score: 289
Period size: 101 Copynumber: 2.4 Consensus size: 102
1167702 AGATGTACAT
* * * * * *
1167712 ACTTACATCGGTGTAAGTATATGTTAAGTGCTACACTTTTTTATTTTGTTTACTTACATCGTTGT
1 ACTTACATCGGTGTAAGTATGTGTTAAGTACTACACTTTTTTATTTTATTCACTTACACCGGTGT
* * *
1167777 AAGTATGTGTTAAATACTACATTTTTTTATTTTATTC
66 AAGTATGTATTAAATACTACACTTGTTTATTTTATTC
* *
1167814 ACTTA-AGTTGGTGT-AGTATGTGTTAAGTACTACACTTTTTTGTTTTATTCACTTACACCGGTG
1 ACTTACA-TCGGTGTAAGTATGTGTTAAGTACTACACTTTTTTATTTTATTCACTTACACCGGTG
* *
1167877 TAAGTTTGTATTAAGTGA-TACACTTGTTTATTTTATTC
65 TAAGTATGTATTAAAT-ACTACACTTGTTTATTTTATTC
* * * * *
1167915 ACTTACACCGATGTAAATATGTGTTAAGTACTATATTTTTTT
1 ACTTACATCGGTGTAAGTATGTGTTAAGTACTACACTTTTTT
1167957 TGTAATAATA
Statistics
Matches: 120, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
101 83 0.69
102 37 0.31
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (102 bp):
ACTTACATCGGTGTAAGTATGTGTTAAGTACTACACTTTTTTATTTTATTCACTTACACCGGTGT
AAGTATGTATTAAATACTACACTTGTTTATTTTATTC
Found at i:1168013 original size:22 final size:21
Alignment explanation
Indices: 1167959--1168013 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 21
1167949 ATTTTTTTTG
*
1167959 TAATAATAGGTTAACCGTAAGC
1 TAATAAT-GGTTAACCGGAAGC
*
1167981 TAAT-AT-G-TAACCGGAACGT
1 TAATAATGGTTAACCGGAA-GC
1168000 TAATAATGGTTAAC
1 TAATAATGGTTAAC
1168014 AATTAGCGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
18 8 0.30
19 6 0.22
20 2 0.07
21 3 0.11
22 8 0.30
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (21 bp):
TAATAATGGTTAACCGGAAGC
Found at i:1194792 original size:2 final size:2
Alignment explanation
Indices: 1194785--1194817 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1194775 ATCCAAAGAG
1194785 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 T
1194818 GATAAGAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1199522 original size:31 final size:31
Alignment explanation
Indices: 1199484--1199557 Score: 139
Period size: 31 Copynumber: 2.4 Consensus size: 31
1199474 ACGTGTTTAG
*
1199484 TACCTAAATTATCAATTTTGGTCTATTTGAA
1 TACCTAAATTATCAATTTTGGTCCATTTGAA
1199515 TACCTAAATTATCAATTTTGGTCCATTTGAA
1 TACCTAAATTATCAATTTTGGTCCATTTGAA
1199546 TACCTAAATTAT
1 TACCTAAATTAT
1199558 AAATATTCGT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.43
Consensus pattern (31 bp):
TACCTAAATTATCAATTTTGGTCCATTTGAA
Found at i:1200503 original size:2 final size:2
Alignment explanation
Indices: 1200496--1200537 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
1200486 CTTTTAATTC
1200496 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C- CT -T CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1200536 CT
1 CT
1200538 TCCTTGGTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1202904 original size:23 final size:23
Alignment explanation
Indices: 1202877--1202932 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
1202867 AAAAGCGTAC
* * *
1202877 CACAAAGATAGAGATAAACGTGT
1 CACAAAGACAAAGATAAACATGT
* *
1202900 CACAAAAACAAAGATAAATATGT
1 CACAAAGACAAAGATAAACATGT
1202923 CACAAAGACA
1 CACAAAGACA
1202933 TAATTATCTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.55, C:0.16, G:0.14, T:0.14
Consensus pattern (23 bp):
CACAAAGACAAAGATAAACATGT
Found at i:1204680 original size:29 final size:29
Alignment explanation
Indices: 1204637--1204719 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
1204627 CTCACCTAAC
1204637 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
1204667 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
1204696 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
1204720 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:1209442 original size:29 final size:29
Alignment explanation
Indices: 1209399--1209481 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
1209389 CTCACCTAAC
1209399 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
1209429 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
1209458 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
1209482 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:1217601 original size:8 final size:8
Alignment explanation
Indices: 1217574--1217639 Score: 53
Period size: 8 Copynumber: 7.6 Consensus size: 8
1217564 CTTTTGGAAA
1217574 TTTAAAAT
1 TTTAAAAT
*
1217582 TATT-ATAT
1 T-TTAAAAT
1217590 TTTAAAAT
1 TTTAAAAT
1217598 TTTAATATAT
1 TTTAA-A-AT
1217608 TTTATTAAAT
1 TTTA--AAAT
1217618 CTTTAAAAT
1 -TTTAAAAT
*
1217627 TTTAAAAG
1 TTTAAAAT
1217635 TTTAA
1 TTTAA
1217640 GCGTGTACTT
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
7 2 0.04
8 25 0.52
9 7 0.15
10 8 0.17
11 5 0.10
12 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (8 bp):
TTTAAAAT
Found at i:1219146 original size:60 final size:60
Alignment explanation
Indices: 1219073--1219209 Score: 161
Period size: 60 Copynumber: 2.3 Consensus size: 60
1219063 AAACTAGGAT
* * * *
1219073 AAAG-TACACAAATGGTCCCTTGACTATAGGGTGTTGCTTTATTGAATC-CTTTAACTATTA
1 AAAGTTACA-AAATGGTCCCCTAACTATAGGATGTTGCTTTATTGAATCTC-TCAACTATTA
** * * *
1219133 AATTTTACAAAATGGTCCCCTAACTATAGGATGTTGCTTTCTTGAGTCTCTCGACTATTA
1 AAAGTTACAAAATGGTCCCCTAACTATAGGATGTTGCTTTATTGAATCTCTCAACTATTA
1219193 AAAGTTACAAAATGGTC
1 AAAGTTACAAAATGGTC
1219210 ATTCAAATAT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
60 59 0.92
61 5 0.08
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.36
Consensus pattern (60 bp):
AAAGTTACAAAATGGTCCCCTAACTATAGGATGTTGCTTTATTGAATCTCTCAACTATTA
Found at i:1221294 original size:2 final size:2
Alignment explanation
Indices: 1221287--1221319 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1221277 ATGAGAAAGG
1221287 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1221320 CATACAAGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1222243 original size:21 final size:21
Alignment explanation
Indices: 1222208--1222248 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1222198 TAGCGTGTCA
* * *
1222208 GTTCACGGTGTTGACGTGACG
1 GTTCACGATGCTGACATGACG
1222229 GTTCACGATGCTGACATGAC
1 GTTCACGATGCTGACATGAC
1222249 ATACAATCTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.22, G:0.32, T:0.27
Consensus pattern (21 bp):
GTTCACGATGCTGACATGACG
Found at i:1228753 original size:60 final size:60
Alignment explanation
Indices: 1228659--1228774 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
1228649 TAGTCCCCTG
* * * * *
1228659 ACTACAGTGTATTGCTTTATTAAGTCCTTTGACTATGAAAAGTTACAGAATGATCATCTA
1 ACTACAGAGTATTGCTTCATTAAGTCCATCGACTATGAAAAGTTACAAAATGATCATCTA
* * *
1228719 ACTACAGAGTGTTGCTTCGTTAAGTCCATCGACTATTAAAAGTTACAAAATGATCA
1 ACTACAGAGTATTGCTTCATTAAGTCCATCGACTATGAAAAGTTACAAAATGATCA
1228775 CTCCACTATT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (60 bp):
ACTACAGAGTATTGCTTCATTAAGTCCATCGACTATGAAAAGTTACAAAATGATCATCTA
Found at i:1229758 original size:7 final size:8
Alignment explanation
Indices: 1229732--1229771 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
1229722 TTTTTAAATT
*
1229732 TAATATTA
1 TAATATAA
1229740 TAATATAA
1 TAATATAA
1229748 TAATA-AA
1 TAATATAA
*
1229755 TAATATTA
1 TAATATAA
1229763 TAATATAA
1 TAATATAA
1229771 T
1 T
1229772 TAACAAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
7 7 0.25
8 21 0.75
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
TAATATAA
Found at i:1235182 original size:5 final size:5
Alignment explanation
Indices: 1235167--1235198 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
1235157 TGTATTAACA
*
1235167 CTTTC CCTTC CTTTC CTTTC CTTTC CTTTC CT
1 CTTTC CTTTC CTTTC CTTTC CTTTC CTTTC CT
1235199 CCAAACATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (5 bp):
CTTTC
Found at i:1237829 original size:36 final size:36
Alignment explanation
Indices: 1237788--1237864 Score: 136
Period size: 36 Copynumber: 2.1 Consensus size: 36
1237778 ACCAAATTAA
1237788 ACGGGGACGAGGAAAAACCGTTTATGCTAAACGGGG
1 ACGGGGACGAGGAAAAACCGTTTATGCTAAACGGGG
* *
1237824 ACGGGGACGGGGAAAAACCGTTTATGTTAAACGGGG
1 ACGGGGACGAGGAAAAACCGTTTATGCTAAACGGGG
1237860 ACGGG
1 ACGGG
1237865 TTTAGTAATC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.31, C:0.16, G:0.39, T:0.14
Consensus pattern (36 bp):
ACGGGGACGAGGAAAAACCGTTTATGCTAAACGGGG
Found at i:1237903 original size:12 final size:12
Alignment explanation
Indices: 1237875--1237911 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
1237865 TTTAGTAATC
*
1237875 CCCGCCCCGATTA
1 CCCGGCCCGA-TA
1237888 CCCGGCCCGATA
1 CCCGGCCCGATA
1237900 CCCGGCCCGATA
1 CCCGGCCCGATA
1237912 AATATTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 14 0.61
13 9 0.39
ACGTcount: A:0.16, C:0.51, G:0.22, T:0.11
Consensus pattern (12 bp):
CCCGGCCCGATA
Found at i:1240211 original size:463 final size:463
Alignment explanation
Indices: 1239160--1241022 Score: 3161
Period size: 463 Copynumber: 4.0 Consensus size: 463
1239150 TATTAAAAGT
* * *
1239160 TATAAAATGATCACTCCAATTATTTATTATGTTATAAACTCGTTCATTTATTTAAAAAAAATATC
1 TATAAAATGATCACTCCAATTATTCATTATGTTATAAACTCGTTCATTTATTTTAAAAAAATATT
* * * *
1239225 AGTATTATGAGCTAAACGTTACTATGTTGACTGTTATGTGATAAAATCAAATCCCAAAATCTCAA
66 GGTATTATGAGCTAAACGTTAATATGTTGAATGTGATGTGATAAAATCAAATCCCAAAATCTCAA
* *
1239290 ATTTTATTTTATCTCAGCCATCATATTAACGTTCAACTTAGACAACCACCGATTCTTTAATGGAA
131 ATTTTATTTTATCTCAGCCATCATATTAAC-TCCAACTTAGACAACCACCGATTCTTTAACGGAA
*
1239355 AAAGATGAGTTTGGAACATAATAAATAATCATGTGATCATTTTGTAACTTTTAATAGTAGAGGGA
195 AAAGATGAGTTTGGAACATAATAAATAATCAGGTGATCATTTTGTAACTTTTAATAGTAGAGGGA
*
1239420 TTTAACAAAGTAACATTCTATAATCGAATGACCATTTTGTAGCTTTCAAAAGTTGGGAGACTTAA
260 TTTAACAAAGTAACATTCTATAATCGAATGACCATTTTGTAGCTTTCAATAGTTGGGAGACTTAA
* *
1239485 TAAAGCAATACTCTATAGTTGGGGGATCATTTGTATATTTTAACTTTTTTTAGTACTTGAGATGA
325 TAAAACAATACTCTATAGTCGGGGGATCATTTGTATATTTTAACTTTTTTTAGTACTTGAGATGA
*
1239550 TTATAAGGTATTATTTGTTCATAATTTCTTTTGTCATCGACAATGTGCACATCTTATAGACACAA
390 TTATAAGGTATTATTTGTTCATAATTTCTTTTGTCATCGACAATGTACACATCTTATAGACACAA
1239615 ATGCTCGAC
455 ATGCTCGAC
1239624 TATAAAATGATCACTCCAATTATTCATTATGTTATAAACTCGTTCATTTATTTTAAAAAAATATT
1 TATAAAATGATCACTCCAATTATTCATTATGTTATAAACTCGTTCATTTATTTTAAAAAAATATT
* * * *
1239689 GGTATTATGAGCTAAATGTTAATATGTTGAATGTGATATAATAAAATCAAATCCCAAAATCTTAA
66 GGTATTATGAGCTAAACGTTAATATGTTGAATGTGATGTGATAAAATCAAATCCCAAAATCTCAA
*
1239754 ATTTTATTTTATCTCAGCCATCATATTAACGTCCAACTTAGACAACCACCGATTCTTTAACGAAA
131 ATTTTATTTTATCTCAGCCATCATATTAAC-TCCAACTTAGACAACCACCGATTCTTTAACGGAA
* *
1239819 AAAGACGAGTTTGGAACATAATAAATAATCAAGTGATCATTTTGTAACTTTTAATAGTAGAGGGA
195 AAAGATGAGTTTGGAACATAATAAATAATCAGGTGATCATTTTGTAACTTTTAATAGTAGAGGGA
*
1239884 TTTAACAAAGTAACATTCTATAATCGAATGACCATTTTGTAGCTTTCAATAGTTGGCAGACTTAA
260 TTTAACAAAGTAACATTCTATAATCGAATGACCATTTTGTAGCTTTCAATAGTTGGGAGACTTAA
* *
1239949 TAAAACCATACTCTATAG-CCGGGGATCATTTGTATATTTTAACTTTTTTTAGTACTTGAGATGA
325 TAAAACAATACTCTATAGTCGGGGGATCATTTGTATATTTTAACTTTTTTTAGTACTTGAGATGA
1240013 TTATAAGGTATTATTTGTTCATAATTTCTTTTGTCATCGACAATGTACACATCTTATAGACACAA
390 TTATAAGGTATTATTTGTTCATAATTTCTTTTGTCATCGACAATGTACACATCTTATAGACACAA
1240078 ATGCTCGAC
455 ATGCTCGAC
* * *
1240087 TATAAAATGATCACTCCAATTATTCATTAGGTTATAAACTCTTTCATTGATTTTAAAAAAATATT
1 TATAAAATGATCACTCCAATTATTCATTATGTTATAAACTCGTTCATTTATTTTAAAAAAATATT
* * *
1240152 GGTATTATGAGCTAAACATTAATATGTTGATTGTGATGTGATAAAATTAAATCCCAAAATCTCAA
66 GGTATTATGAGCTAAACGTTAATATGTTGAATGTGATGTGATAAAATCAAATCCCAAAATCTCAA
* *
1240217 ATTTTATTTTATCTCAACCATCATGTTAACTCCAACTTAGACAACCACCGATTCTTTAACGGAAA
131 ATTTTATTTTATCTCAGCCATCATATTAACTCCAACTTAGACAACCACCGATTCTTTAACGGAAA
* *
1240282 AAGATGAGTTTGGAGCATAATAAATAATCAGGTGATCATTTTGTAACTTTTAATAGTATAGGGAT
196 AAGATGAGTTTGGAACATAATAAATAATCAGGTGATCATTTTGTAACTTTTAATAGTAGAGGGAT
* *
1240347 TTAACAAAGTAACATTCTATAATCGAATGATCATTTTGTAGCTTTTAATAGTTGGGAGACTTAAT
261 TTAACAAAGTAACATTCTATAATCGAATGACCATTTTGTAGCTTTCAATAGTTGGGAGACTTAAT
* * * *
1240412 AAAGCATTATTCTATAGTCGGGGGATCATTTGTATATTTTAACTTTTTTTAGTACTTGAGGTGAT
326 AAAACAATACTCTATAGTCGGGGGATCATTTGTATATTTTAACTTTTTTTAGTACTTGAGATGAT
1240477 TATAAGGTATTATTTGTTCATAATTTCTTTTGTCATCGACAATGTACACATCTTATAGACACAAA
391 TATAAGGTATTATTTGTTCATAATTTCTTTTGTCATCGACAATGTACACATCTTATAGACACAAA
1240542 TGCTCGAC
456 TGCTCGAC
* *
1240550 TATAAAATGATCACTCCAATTATTCATTATGCTATAAACTCGTTCGTTTATTTTAAAAAAATATT
1 TATAAAATGATCACTCCAATTATTCATTATGTTATAAACTCGTTCATTTATTTTAAAAAAATATT
*
1240615 GGTATTATGAGCTAAATGTTAATATGTTGAATGTGATGTGATAAAATCAAATCCCAAAATCTCAA
66 GGTATTATGAGCTAAACGTTAATATGTTGAATGTGATGTGATAAAATCAAATCCCAAAATCTCAA
* *
1240680 ATTTTATTTTATCTCAGCAATCATGTTAACTCCAACTTAGACAACCACCGATTCTTTAACGGAAA
131 ATTTTATTTTATCTCAGCCATCATATTAACTCCAACTTAGACAACCACCGATTCTTTAACGGAAA
* * * *
1240745 AAGATGAGATTGGAACATAATAAATAATCAGGTGATTAATTTGTAACTTTTAATAGTATAGGGAT
196 AAGATGAGTTTGGAACATAATAAATAATCAGGTGATCATTTTGTAACTTTTAATAGTAGAGGGAT
* * *
1240810 TTAACAAAGTAACATTCTATAATCGAATGATCATTTTGTAGCTTTTAATAGTTGTGAGACTTAAT
261 TTAACAAAGTAACATTCTATAATCGAATGACCATTTTGTAGCTTTCAATAGTTGGGAGACTTAAT
* * * *
1240875 AAAGCAATATTCTATAGTCGGGGGATCATTTGCATATTTTAACTTTTTTTTTAGTACTTGAGGTG
326 AAAACAATACTCTATAGTCGGGGGATCATTTGTATATTTTAAC--TTTTTTTAGTACTTGAGATG
1240940 ATTATAAGGTATTATTTGTTCATAATTTCTTTTGTCATCGACAATGTACACATCTTATAGACACA
389 ATTATAAGGTATTATTTGTTCATAATTTCTTTTGTCATCGACAATGTACACATCTTATAGACACA
*
1241005 AATGCTCGAA
454 AATGCTCGAC
*
1241015 TTTAAAAT
1 TATAAAAT
1241023 CTTTAAGAAA
Statistics
Matches: 1327, Mismatches: 69, Indels: 5
0.95 0.05 0.00
Matches are distributed among these distances:
462 170 0.13
463 733 0.55
464 323 0.24
465 101 0.08
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (463 bp):
TATAAAATGATCACTCCAATTATTCATTATGTTATAAACTCGTTCATTTATTTTAAAAAAATATT
GGTATTATGAGCTAAACGTTAATATGTTGAATGTGATGTGATAAAATCAAATCCCAAAATCTCAA
ATTTTATTTTATCTCAGCCATCATATTAACTCCAACTTAGACAACCACCGATTCTTTAACGGAAA
AAGATGAGTTTGGAACATAATAAATAATCAGGTGATCATTTTGTAACTTTTAATAGTAGAGGGAT
TTAACAAAGTAACATTCTATAATCGAATGACCATTTTGTAGCTTTCAATAGTTGGGAGACTTAAT
AAAACAATACTCTATAGTCGGGGGATCATTTGTATATTTTAACTTTTTTTAGTACTTGAGATGAT
TATAAGGTATTATTTGTTCATAATTTCTTTTGTCATCGACAATGTACACATCTTATAGACACAAA
TGCTCGAC
Found at i:1240424 original size:60 final size:60
Alignment explanation
Indices: 1240314--1240427 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
1240304 AATAATCAGG
* *
1240314 TGATCATTTTGTAACTTTTAATAGTATAGGGATTTAACAAAGTAACATTCTATAATCGAA
1 TGATCATTTTGTAACTTTTAATAGTATAGGGACTTAACAAAGCAACATTCTATAATCGAA
* * * **
1240374 TGATCATTTTGTAGCTTTTAATAGT-TGGGAGACTTAATAAAGCATTATTCTATA
1 TGATCATTTTGTAACTTTTAATAGTATAGG-GACTTAACAAAGCAACATTCTATA
1240428 GTCGGGGGAT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
59 3 0.07
60 43 0.93
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (60 bp):
TGATCATTTTGTAACTTTTAATAGTATAGGGACTTAACAAAGCAACATTCTATAATCGAA
Found at i:1240439 original size:60 final size:60
Alignment explanation
Indices: 1240315--1240442 Score: 141
Period size: 60 Copynumber: 2.1 Consensus size: 60
1240305 ATAATCAGGT
* * *
1240315 GATCATTTTGTAACTTTTAATAGTATAGGGATTTAACAAAGTAACATTCTATAATCGAAT
1 GATCATTTTGTAACTTTTAATAGTATAGGGACTTAACAAAGCAACATTCTATAATCGAAG
* * * ** * **
1240375 GATCATTTTGTAGCTTTTAATAGT-TGGGAGACTTAATAAAGCATTATTCTATAGTCGGGG
1 GATCATTTTGTAACTTTTAATAGTATAGG-GACTTAACAAAGCAACATTCTATAATCGAAG
1240435 GATCATTT
1 GATCATTT
1240443 GTATATTTTA
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
59 3 0.05
60 53 0.95
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (60 bp):
GATCATTTTGTAACTTTTAATAGTATAGGGACTTAACAAAGCAACATTCTATAATCGAAG
Found at i:1242753 original size:21 final size:21
Alignment explanation
Indices: 1242727--1242776 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1242717 TCCAGATTCA
1242727 CAACGCGAACATCGACTATCG
1 CAACGCGAACATCGACTATCG
* *
1242748 CAACGCGAACTTTGACTATCG
1 CAACGCGAACATCGACTATCG
*
1242769 CAATGCGA
1 CAACGCGA
1242777 TTTTCCAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.32, C:0.30, G:0.20, T:0.18
Consensus pattern (21 bp):
CAACGCGAACATCGACTATCG
Found at i:1242796 original size:19 final size:19
Alignment explanation
Indices: 1242772--1242838 Score: 71
Period size: 21 Copynumber: 3.3 Consensus size: 19
1242762 ACTATCGCAA
1242772 TGCGATTTTCCAAATTCGT
1 TGCGATTTTCCAAATTCGT
** *
1242791 TGCGATAGTCCAAGTTCGCGT
1 TGCGATTTTCCAAATT--CGT
1242812 TGCGATTTATTCCAAATTCGT
1 TGCGA-TT-TTCCAAATTCGT
1242833 TGCGAT
1 TGCGAT
1242839 AGTCCAAGTT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
19 13 0.34
20 1 0.03
21 16 0.42
22 1 0.03
23 7 0.18
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (19 bp):
TGCGATTTTCCAAATTCGT
Found at i:1242814 original size:21 final size:21
Alignment explanation
Indices: 1242788--1242867 Score: 92
Period size: 21 Copynumber: 3.8 Consensus size: 21
1242778 TTTCCAAATT
1242788 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* *
1242809 CGTTGCGATTTATTCCAAATT--
1 CGTTGCGA--TAGTCCAAGTTCG
1242830 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* *
1242851 CTTTGAGATAGTCCAAG
1 CGTTGCGATAGTCCAAG
1242868 ACCACGACCA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
19 9 0.18
21 31 0.63
23 9 0.18
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.33
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGTTCG
Found at i:1242829 original size:42 final size:40
Alignment explanation
Indices: 1242772--1242851 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 40
1242762 ACTATCGCAA
1242772 TGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1 TGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1242812 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGC
1 TGCGA-TT-TTCCAAATTCGTTGCGATAGTCCAAGTTCGC
1242852 TTTGAGATAG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
40 5 0.13
41 2 0.05
42 31 0.82
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (40 bp):
TGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
Found at i:1242906 original size:5 final size:6
Alignment explanation
Indices: 1242867--1242903 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
1242857 GATAGTCCAA
1242867 GACCAC GACCAC GACCAC GACCAC G-CCAC GA-CAC GAC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GAC
1242904 ACGGACGGCG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 10 0.34
6 19 0.66
ACGTcount: A:0.32, C:0.49, G:0.19, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:1243069 original size:24 final size:24
Alignment explanation
Indices: 1243037--1243082 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
1243027 CATTACCAAC
1243037 ACTTGTTCCCAATACTATGTGGAT
1 ACTTGTTCCCAATACTATGTGGAT
1243061 ACTTGTTCCCAATACTATGTGG
1 ACTTGTTCCCAATACTATGTGG
1243083 GATTGAGCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (24 bp):
ACTTGTTCCCAATACTATGTGGAT
Found at i:1243577 original size:5 final size:5
Alignment explanation
Indices: 1243569--1243595 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1243559 TCGGGTCATG
1243569 GAGTA GAGTA GAGTA GAGTA GAGTA GA
1 GAGTA GAGTA GAGTA GAGTA GAGTA GA
1243596 AGCCACCGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.41, T:0.19
Consensus pattern (5 bp):
GAGTA
Found at i:1245093 original size:31 final size:31
Alignment explanation
Indices: 1245058--1245123 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
1245048 AAACTATCAG
1245058 TTTTGGTTCGTTTTAGTACATAAACTTTAAT
1 TTTTGGTTCGTTTTAGTACATAAACTTTAAT
* *
1245089 TTTTGGTTCGTTTTAGTACCTAAACTTTCAT
1 TTTTGGTTCGTTTTAGTACATAAACTTTAAT
1245120 TTTT
1 TTTT
1245124 TAAGAACATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.21, C:0.12, G:0.12, T:0.55
Consensus pattern (31 bp):
TTTTGGTTCGTTTTAGTACATAAACTTTAAT
Found at i:1250040 original size:24 final size:22
Alignment explanation
Indices: 1250004--1250055 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 22
1249994 GAGTGATGTA
1250004 ATTTGTTCTTACATCTCCATTG
1 ATTTGTTCTTACATCTCCATTG
*
1250026 ATTTGTGTCCTTACATCTCTATTG
1 ATTTGT-T-CTTACATCTCCATTG
*
1250050 AATTGT
1 ATTTGT
1250056 CTGAGGCCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 6 0.23
23 1 0.04
24 19 0.73
ACGTcount: A:0.19, C:0.19, G:0.12, T:0.50
Consensus pattern (22 bp):
ATTTGTTCTTACATCTCCATTG
Found at i:1251359 original size:32 final size:32
Alignment explanation
Indices: 1251321--1251389 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 32
1251311 CTCGTGTTCA
* * *
1251321 TTAAGAAAATTTGTGGCTCGACTCGTTGCTCG
1 TTAAGAAAATTTGTGACTCGACTCATTGCTAG
*
1251353 TTAAGAAAATTTGTTACTCGACTCATTGCTAG
1 TTAAGAAAATTTGTGACTCGACTCATTGCTAG
1251385 TTAAG
1 TTAAG
1251390 CTCGTTACTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (32 bp):
TTAAGAAAATTTGTGACTCGACTCATTGCTAG
Found at i:1253754 original size:45 final size:45
Alignment explanation
Indices: 1253578--1253750 Score: 283
Period size: 45 Copynumber: 3.8 Consensus size: 45
1253568 GCTTCAACTT
*
1253578 GTTAGGCATGTCATACATGGATCATGTGAGATGAACTACCATAAA
1 GTTAGACATGTCATACATGGATCATGTGAGATGAACTACCATAAA
1253623 GTTAGACATGTCATACATGGATCATGTGAGATGAACTACCATAAA
1 GTTAGACATGTCATACATGGATCATGTGAGATGAACTACCATAAA
* *
1253668 GTTAGATATGTCATACATGGATCATGTGAGATGAACTATCATAAA
1 GTTAGACATGTCATACATGGATCATGTGAGATGAACTACCATAAA
* * * *
1253713 GTTAGACATGTCATACATAGACCACGTGAGATAAACTA
1 GTTAGACATGTCATACATGGATCATGTGAGATGAACTA
1253751 TCATGCCCCT
Statistics
Matches: 120, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 120 1.00
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (45 bp):
GTTAGACATGTCATACATGGATCATGTGAGATGAACTACCATAAA
Found at i:1257665 original size:29 final size:29
Alignment explanation
Indices: 1257620--1257681 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
1257610 TTCTACAGTA
* *
1257620 ACCTTGGAGGTCGCCATGGCATCCGGGCG
1 ACCTTGGAGGTCACCATGGCATCCGAGCG
1257649 ACCTTGGAGGTCACCATGGCATCCGAGCG
1 ACCTTGGAGGTCACCATGGCATCCGAGCG
1257678 ACCT
1 ACCT
1257682 GTGTGGTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.18, C:0.32, G:0.32, T:0.18
Consensus pattern (29 bp):
ACCTTGGAGGTCACCATGGCATCCGAGCG
Found at i:1257766 original size:20 final size:20
Alignment explanation
Indices: 1257741--1257813 Score: 67
Period size: 20 Copynumber: 3.4 Consensus size: 20
1257731 GTATTGGAGC
1257741 ATGCATGGGGGAGTTGTGGG
1 ATGCATGGGGGAGTTGTGGG
*
1257761 ATGCATGCTGTGCATGG-GATGTGGG
1 ATGCATG--G-G---GGAGTTGTGGG
1257786 AATGCATGGGGGAGTTGTGGG
1 -ATGCATGGGGGAGTTGTGGG
1257807 ATGCATG
1 ATGCATG
1257814 TTGTGCATGG
Statistics
Matches: 43, Mismatches: 2, Indels: 16
0.70 0.03 0.26
Matches are distributed among these distances:
20 16 0.37
21 7 0.16
22 1 0.02
23 2 0.05
24 1 0.02
25 7 0.16
26 9 0.21
ACGTcount: A:0.18, C:0.08, G:0.48, T:0.26
Consensus pattern (20 bp):
ATGCATGGGGGAGTTGTGGG
Found at i:1257791 original size:46 final size:46
Alignment explanation
Indices: 1257741--1257833 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 46
1257731 GTATTGGAGC
*
1257741 ATGCATGGGGGAGTTGTGGGATGCATGCTGTGCATGGGATGTGGGA
1 ATGCATGGGGGAGTTGTGGGATGCATGCTGTGCATGGGACGTGGGA
*
1257787 ATGCATGGGGGAGTTGTGGGATGCATGTTGTGCATGGGACGTGGGA
1 ATGCATGGGGGAGTTGTGGGATGCATGCTGTGCATGGGACGTGGGA
1257833 A
1 A
1257834 CTGTGCATGG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.18, C:0.09, G:0.47, T:0.26
Consensus pattern (46 bp):
ATGCATGGGGGAGTTGTGGGATGCATGCTGTGCATGGGACGTGGGA
Found at i:1258367 original size:21 final size:21
Alignment explanation
Indices: 1258342--1258385 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1258332 AATCTAGTTA
1258342 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
1258363 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
1258384 AT
1 AT
1258386 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:1258395 original size:28 final size:30
Alignment explanation
Indices: 1258362--1258424 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
1258352 TAGTATAAAT
*
1258362 TATTAGTTTGTTAGTTTAAG-T-TATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
1258390 TATTAGTTTATTAGTTTAAGTTATATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
1258420 TATTA
1 TATTA
1258425 TATAAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 19 0.59
29 1 0.03
30 12 0.38
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (30 bp):
TATTAGTTTATTAGTTTAAGTTATATATTA
Found at i:1259264 original size:26 final size:25
Alignment explanation
Indices: 1259235--1259293 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
1259225 AAATCATATT
*
1259235 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
1259261 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
1259287 ATTATTA
1 ATTATTA
1259294 GGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:1262151 original size:11 final size:11
Alignment explanation
Indices: 1262135--1262407 Score: 72
Period size: 11 Copynumber: 22.3 Consensus size: 11
1262125 TCATTATCAA
1262135 AATGATTTAAT
1 AATGATTTAAT
1262146 AATGATTT-A-
1 AATGATTTAAT
1262155 AAT-ATTTAAT
1 AATGATTTAAT
*
1262165 GATTTGATGATTTAGT
1 -A----ATGATTTAAT
1262181 AATGATTTGATAAT
1 AATGA-TT--TAAT
* *
1262195 AATCATTATAGT
1 AATGATT-TAAT
1262207 AATGATTTGATAAT
1 AATGA-TT--TAAT
*
1262221 AATCATTATAAT
1 AATGATT-TAAT
1262233 AATGATTTAGTAAT
1 AATGA-TT--TAAT
* *
1262247 AATCATTATAAA
1 AATGATT-TAAT
1262259 AATGATTTAAT
1 AATGATTTAAT
1262270 AATGATTT-A-
1 AATGATTTAAT
1262279 AAT-ATTTAAT
1 AATGATTTAAT
*
1262289 GATTTGATGATTTAGT
1 -A----ATGATTTAAT
1262305 AATGATTTGATAAT
1 AATGA-TT--TAAT
*
1262319 AATCATTATAAT
1 AATGATT-TAAT
1262331 AATGATTTTATAAT
1 AATGA--TT-TAAT
* *
1262345 AATTATTTAGT
1 AATGATTTAAT
* * *
1262356 TATTATTTAGT
1 AATGATTTAAT
*
1262367 AATTATTTATAAT
1 AATGA-TT-TAAT
1262380 AATGATTTAATACT
1 AATGATTT-A-A-T
1262394 AATGATTTAAT
1 AATGATTTAAT
1262405 AAT
1 AAT
1262408 TATTACTAAT
Statistics
Matches: 205, Mismatches: 24, Indels: 66
0.69 0.08 0.22
Matches are distributed among these distances:
8 8 0.04
9 8 0.04
10 2 0.01
11 51 0.25
12 47 0.23
13 21 0.10
14 50 0.24
15 6 0.03
16 12 0.06
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (11 bp):
AATGATTTAAT
Found at i:1262206 original size:26 final size:26
Alignment explanation
Indices: 1262177--1262355 Score: 162
Period size: 26 Copynumber: 7.2 Consensus size: 26
1262167 TTTGATGATT
1262177 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
1262203 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
1262229 TAATAATGATTT-AGTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
** *
1262255 TAAAAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * *
1262277 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
1262301 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
* * *
1262327 TAATAATGATTTTATAATAATTATT-
1 TAGTAATGATTTGATAATAATCATTA
1262352 TAGT
1 TAGT
1262356 TATTATTTAG
Statistics
Matches: 130, Mismatches: 13, Indels: 21
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.01
20 5 0.04
22 3 0.02
23 11 0.08
24 9 0.07
25 12 0.09
26 83 0.64
27 6 0.05
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (26 bp):
TAGTAATGATTTGATAATAATCATTA
Found at i:1262344 original size:124 final size:123
Alignment explanation
Indices: 1262122--1262391 Score: 436
Period size: 124 Copynumber: 2.2 Consensus size: 123
1262112 ATGTATTTAT
*
1262122 TAATCATTATCAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
*
1262187 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAATAATGATTTGATAATAATCATT-TAATAATGATTTAGTAA
1262246 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
* * * * *
1262311 TTGATAATAATCATTATAATAATGATTTTATAATAATTATTTAGTTATTATTTAGTAA
66 TTGATAATAATCATTATAATAATGATTTGATAATAATCATTTAATAATGATTTAGTAA
* *
1262369 TTAT--TTATAATAATGATTTAATA
1 TAATCATTATAAAAATGATTTAATA
1262392 CTAATGATTT
Statistics
Matches: 137, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
121 18 0.13
123 17 0.12
124 102 0.74
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (123 bp):
TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
TTGATAATAATCATTATAATAATGATTTGATAATAATCATTTAATAATGATTTAGTAA
Found at i:1262398 original size:14 final size:14
Alignment explanation
Indices: 1262180--1262407 Score: 105
Period size: 14 Copynumber: 17.1 Consensus size: 14
1262170 GATGATTTAG
*
1262180 TAATGATTTGATAA
1 TAATGATTTAATAA
* *
1262194 TAATCA-TT-ATAG
1 TAATGATTTAATAA
*
1262206 TAATGATTTGATAA
1 TAATGATTTAATAA
*
1262220 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
1262232 TAATGATTTAGTAA
1 TAATGATTTAATAA
*
1262246 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
1262258 AAATGA-TT--TAA
1 TAATGATTTAATAA
*
1262269 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
*
1262285 TAATGATTTGATGATTTAG
1 TAATGATTT-A--A--TAA
*
1262304 TAATGATTTGATAA
1 TAATGATTTAATAA
*
1262318 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
1262330 TAATGATTTTATAA
1 TAATGATTTAATAA
* *
1262344 TAATTATTTAGT--
1 TAATGATTTAATAA
* *
1262356 T-ATTATTTAGTAA
1 TAATGATTTAATAA
1262369 T--T-ATTT-ATAA
1 TAATGATTTAATAA
*
1262379 TAATGATTTAATAC
1 TAATGATTTAATAA
1262393 TAATGATTTAATAA
1 TAATGATTTAATAA
1262407 T
1 T
1262408 TATTACTAAT
Statistics
Matches: 168, Mismatches: 25, Indels: 42
0.71 0.11 0.18
Matches are distributed among these distances:
10 4 0.02
11 22 0.13
12 40 0.24
13 19 0.11
14 58 0.35
15 2 0.01
16 11 0.07
18 1 0.01
19 9 0.05
20 2 0.01
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:1262430 original size:38 final size:38
Alignment explanation
Indices: 1262360--1262433 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
1262350 TTTAGTTATT
* **
1262360 ATTTAGTAATTATTTATAATAATGATTTAATACTAATG
1 ATTTAATAATTATTTATAATAATGATAGAATACTAATG
*
1262398 ATTTAATAATTA-TTACTAATAATTATAGAATACTAA
1 ATTTAATAATTATTTA-TAATAATGATAGAATACTAA
1262434 CAAATGAGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 3 0.10
38 28 0.90
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (38 bp):
ATTTAATAATTATTTATAATAATGATAGAATACTAATG
Found at i:1262640 original size:17 final size:17
Alignment explanation
Indices: 1262615--1262647 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1262605 ACTAAATATT
*
1262615 TAATTATTTGATACTAG
1 TAATGATTTGATACTAG
1262632 TAATGATTTGATACTA
1 TAATGATTTGATACTA
1262648 AAAATCATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (17 bp):
TAATGATTTGATACTAG
Found at i:1262640 original size:25 final size:23
Alignment explanation
Indices: 1262561--1262640 Score: 67
Period size: 24 Copynumber: 3.3 Consensus size: 23
1262551 GATTTATTGT
1262561 TAATATTTAATTATTTGATAC--
1 TAATATTTAATTATTTGATACTA
* *
1262582 TAATGATTTAAAATAGTTGATTTACTA
1 TAAT-ATTT-AATTATTTGA--TACTA
1262609 -AATATTTAATTATTTGATACTA
1 TAATATTTAATTATTTGATACTA
1262631 GTAATGATTT
1 -TAAT-ATTT
1262641 GATACTAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
21 4 0.09
22 9 0.20
23 8 0.17
24 11 0.24
25 11 0.24
26 3 0.07
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.49
Consensus pattern (23 bp):
TAATATTTAATTATTTGATACTA
Found at i:1264823 original size:15 final size:14
Alignment explanation
Indices: 1264800--1264830 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
1264790 TACAACACTA
1264800 AACTTTAATATAAT
1 AACTTTAATATAAT
1264814 AACTTATAATATAAT
1 AACTT-TAATATAAT
1264829 AA
1 AA
1264831 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:1264955 original size:34 final size:32
Alignment explanation
Indices: 1264891--1264972 Score: 89
Period size: 34 Copynumber: 2.6 Consensus size: 32
1264881 GCTAAACCCT
* *
1264891 TAAAC-AACTAATAAAATATTCTTTTATATAA
1 TAAACTAACTAATAAACTATTCTTTCATATAA
1264922 CTAAAACTAACTAATAAACTATT-TTTCATTATAA
1 -T-AAACTAACTAATAAACTATTCTTTCA-TATAA
*
1264956 TATACT-ACTAATAAACT
1 TAAACTAACTAATAAACT
1264973 TACTAACTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
31 11 0.25
32 5 0.11
33 9 0.20
34 19 0.43
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (32 bp):
TAAACTAACTAATAAACTATTCTTTCATATAA
Found at i:1265089 original size:45 final size:45
Alignment explanation
Indices: 1265012--1265144 Score: 136
Period size: 45 Copynumber: 3.0 Consensus size: 45
1265002 TCAACAAACA
*
1265012 AATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTT
1 AATATAAC-TAACTA-TTAAC-AAAACAAACTAATTAAATAATTTTTT
* *
1265060 TATATAACTAACTATTAACAAAACAAACTAATT-AATTATTTTTT
1 AATATAACTAACTATTAACAAAACAAACTAATTAAATAATTTTTT
1265104 AACTAT-A-TAACTA-T--C-AAACATATACTAATTAAATAATTTTT
1 AA-TATAACTAACTATTAACAAAACA-A-ACTAATTAAATAATTTTT
1265145 AATTTAGGTA
Statistics
Matches: 76, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
39 5 0.07
40 2 0.03
41 7 0.09
42 10 0.13
43 6 0.08
44 12 0.16
45 16 0.21
46 5 0.07
47 6 0.08
48 7 0.09
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (45 bp):
AATATAACTAACTATTAACAAAACAAACTAATTAAATAATTTTTT
Found at i:1265707 original size:29 final size:29
Alignment explanation
Indices: 1265665--1265767 Score: 179
Period size: 29 Copynumber: 3.6 Consensus size: 29
1265655 GACTACATGG
1265665 GACTACATGGCGACCTACAAGGTCGCCGA
1 GACTACATGGCGACCTACAAGGTCGCCGA
*
1265694 GACTACATGGCGACCTACAAGGTCGCCGG
1 GACTACATGGCGACCTACAAGGTCGCCGA
*
1265723 GACTACATGGCGACCTACAAGGTCGCCTA
1 GACTACATGGCGACCTACAAGGTCGCCGA
*
1265752 GGCTACATGGCGACCT
1 GACTACATGGCGACCT
1265768 CTCTATTGGC
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 70 1.00
ACGTcount: A:0.25, C:0.31, G:0.28, T:0.16
Consensus pattern (29 bp):
GACTACATGGCGACCTACAAGGTCGCCGA
Found at i:1265817 original size:21 final size:21
Alignment explanation
Indices: 1265791--1265837 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
1265781 TATATGGCTT
1265791 GTATGGCTCGTATGTCACCCC
1 GTATGGCTCGTATGTCACCCC
1265812 GTATGGCTCGTATGTCACCCC
1 GTATGGCTCGTATGTCACCCC
1265833 GTATG
1 GTATG
1265838 TCGCCTGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.15, C:0.30, G:0.26, T:0.30
Consensus pattern (21 bp):
GTATGGCTCGTATGTCACCCC
Found at i:1274110 original size:31 final size:31
Alignment explanation
Indices: 1274072--1274133 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
1274062 CTGGTGTAGG
*
1274072 TGAATTCATCACCTACGAGTTTTCTAATACT
1 TGAATTCATCACCTACGAATTTTCTAATACT
1274103 TGAATTCATCACCTACGAATTTTCTAATACT
1 TGAATTCATCACCTACGAATTTTCTAATACT
1274134 GTAACATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.39
Consensus pattern (31 bp):
TGAATTCATCACCTACGAATTTTCTAATACT
Found at i:1277779 original size:15 final size:16
Alignment explanation
Indices: 1277759--1277789 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1277749 GTAAGGGCAG
1277759 ATGAAGAA-CAACATC
1 ATGAAGAACCAACATC
1277774 ATGAAGAACCAACATC
1 ATGAAGAACCAACATC
1277790 GGGTTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.52, C:0.23, G:0.13, T:0.13
Consensus pattern (16 bp):
ATGAAGAACCAACATC
Found at i:1284411 original size:42 final size:42
Alignment explanation
Indices: 1284346--1284458 Score: 199
Period size: 42 Copynumber: 2.7 Consensus size: 42
1284336 ATACTTAGAA
*
1284346 TAATACTAAACCACATGGCTATTATCAGCACCTAAGGATAAG
1 TAATACTAAACCACAAGGCTATTATCAGCACCTAAGGATAAG
*
1284388 TAATACTAAACCACAAGGTTATTATCAGCACCTAAGGATAAG
1 TAATACTAAACCACAAGGCTATTATCAGCACCTAAGGATAAG
*
1284430 TAATACTAAACCACACGGCTATTATCAGC
1 TAATACTAAACCACAAGGCTATTATCAGC
1284459 TTAGTTTTAA
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 67 1.00
ACGTcount: A:0.41, C:0.22, G:0.13, T:0.24
Consensus pattern (42 bp):
TAATACTAAACCACAAGGCTATTATCAGCACCTAAGGATAAG
Found at i:1294690 original size:522 final size:522
Alignment explanation
Indices: 1293706--1294750 Score: 1955
Period size: 522 Copynumber: 2.0 Consensus size: 522
1293696 TTCTTCAACT
* *
1293706 TCCTCTTTAACATCTTTCCCTTCACTACCTTCACTGTCAGAACTTTGTTTCCTTGCTCTGCCCCT
1 TCCTCTTTAACATCTTTCCCTTCACTACCTTCAATGTCAGAACATTGTTTCCTTGCTCTGCCCCT
*
1293771 TCTTGCTCTCTTCTTTTGGGGCATCCCATTCTCTCCACTTTCATTGTGATCATCTTCTTGTTGTT
66 TCTTGCTCTCTTCTTCTGGGGCATCCCATTCTCTCCACTTTCATTGTGATCATCTTCTTGTTGTT
* * *
1293836 CGGAACGAACCACTTTCCTCTTTTTCCTGCCCCTCCGTCTGCCCTTCTTTTCCACAAGTTCTTCA
131 CAGAACGAACCACTTTCCTCTTCTTCCTGCCCATCCGTCTGCCCTTCTTTTCCACAAGTTCTTCA
* *
1293901 TCTTCATATAGAACCTCAGCATAACTAACCCTCTTAGAAACTGCTCTCAGTCTATTCTTCAAATC
196 TCTTCATATAGAACCTCAGCATAACTAAACCTCTTAGAAACTGCTCTCAGCCTATTCTTCAAATC
* *
1293966 ATCCCCACTATTACCTTGCCCATTAACAGCAGCAGCCAAGCAAGCTTCTTCTTTCGTACAATTTC
261 ACCCCCACTATTACCTTGCCCATTAACAGCAGCAGCCAAACAAGCTTCTTCTTTCGTACAATTTC
1294031 CATCATCTCCGTCTGCTATCTCTAGATTATCAACAGGAGTCGTTCTTTCCTCCAATTTCTCCCCA
326 CATCATCTCCGTCTGCTATCTCTAGATTATCAACAGGAGTCGTTCTTTCCTCCAATTTCTCCCCA
*
1294096 CTCTTTCCCTCTTGGGCAACCTCCTTCTCGCCCTTCCTTGAAGCACCTGTCACCCCCTTCTTTCG
391 CTCCTTCCCTCTTGGGCAACCTCCTTCTCGCCCTTCCTTGAAGCACCTGTCACCCCCTTCTTTCG
* *
1294161 ACCTCTCTTCTTAGGCTTATTCAAAGTATCCCCTTCTATATCCATCTTCCCGTCTCCTTCAATCC
456 ACCTCTCTTCTTAAGCTTATTCAAAGCATCCCCTTCTATATCCATCTTCCCGTCTCCTTCAATCC
1294226 CC
521 CC
1294228 TCCTCTTTAACATCTTTCCCTTCACTACCTTCAATGTCAGAACATTGTTTCCTTGCTCTGCCCCT
1 TCCTCTTTAACATCTTTCCCTTCACTACCTTCAATGTCAGAACATTGTTTCCTTGCTCTGCCCCT
1294293 TCTTGCTCTCTTCTTCTGGGGCATCCCATTCTCTCCACTTTCATTGTGATCATCTTCTTGTTGTT
66 TCTTGCTCTCTTCTTCTGGGGCATCCCATTCTCTCCACTTTCATTGTGATCATCTTCTTGTTGTT
1294358 CAGAACGAACCACTTTCCTCTTCTTCCTGCCCATCCGTCTGCCCTTCTTTTCCACAAGTTCTTCA
131 CAGAACGAACCACTTTCCTCTTCTTCCTGCCCATCCGTCTGCCCTTCTTTTCCACAAGTTCTTCA
1294423 TCTTCATATAGAACCTCAGCATAACTAAACCTCTTAGAAACTGCTCTCAGCCTATTCTTCAAATC
196 TCTTCATATAGAACCTCAGCATAACTAAACCTCTTAGAAACTGCTCTCAGCCTATTCTTCAAATC
* *
1294488 ACCCCCACTATTTCCTTGCCCATTAACAGCAGCAGCCAAACAATCTTCTTCTTTCGTACAATTTC
261 ACCCCCACTATTACCTTGCCCATTAACAGCAGCAGCCAAACAAGCTTCTTCTTTCGTACAATTTC
1294553 CATCATCTCCGTCTGCTATCTCTAGATTATCAACAGGAGTCGTTCTTTCCTCCAATTTCTCCCCA
326 CATCATCTCCGTCTGCTATCTCTAGATTATCAACAGGAGTCGTTCTTTCCTCCAATTTCTCCCCA
1294618 CTCCTTCCCTCTTGGGCAACCTCCTTCTCGCCCTTCCTTGAAGCACCTGTCACCCCCTTCTTTCG
391 CTCCTTCCCTCTTGGGCAACCTCCTTCTCGCCCTTCCTTGAAGCACCTGTCACCCCCTTCTTTCG
1294683 ACCTCTCTTCTTAAGCTTATTCAAAGCATCCCCTTCTATATCCATCTTCCCGTCTCCTTCAATCC
456 ACCTCTCTTCTTAAGCTTATTCAAAGCATCCCCTTCTATATCCATCTTCCCGTCTCCTTCAATCC
1294748 CC
521 CC
1294750 T
1 T
1294751 TCTCCTCTTC
Statistics
Matches: 508, Mismatches: 15, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
522 508 1.00
ACGTcount: A:0.18, C:0.36, G:0.10, T:0.36
Consensus pattern (522 bp):
TCCTCTTTAACATCTTTCCCTTCACTACCTTCAATGTCAGAACATTGTTTCCTTGCTCTGCCCCT
TCTTGCTCTCTTCTTCTGGGGCATCCCATTCTCTCCACTTTCATTGTGATCATCTTCTTGTTGTT
CAGAACGAACCACTTTCCTCTTCTTCCTGCCCATCCGTCTGCCCTTCTTTTCCACAAGTTCTTCA
TCTTCATATAGAACCTCAGCATAACTAAACCTCTTAGAAACTGCTCTCAGCCTATTCTTCAAATC
ACCCCCACTATTACCTTGCCCATTAACAGCAGCAGCCAAACAAGCTTCTTCTTTCGTACAATTTC
CATCATCTCCGTCTGCTATCTCTAGATTATCAACAGGAGTCGTTCTTTCCTCCAATTTCTCCCCA
CTCCTTCCCTCTTGGGCAACCTCCTTCTCGCCCTTCCTTGAAGCACCTGTCACCCCCTTCTTTCG
ACCTCTCTTCTTAAGCTTATTCAAAGCATCCCCTTCTATATCCATCTTCCCGTCTCCTTCAATCC
CC
Found at i:1296756 original size:15 final size:15
Alignment explanation
Indices: 1296733--1296766 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1296723 ATATTTAACT
* *
1296733 GGGCGGGCGGATGTG
1 GGGCAGGCGGATGCG
1296748 GGGCAGGCGGATGCG
1 GGGCAGGCGGATGCG
1296763 GGGC
1 GGGC
1296767 GGGTAATATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.18, G:0.65, T:0.09
Consensus pattern (15 bp):
GGGCAGGCGGATGCG
Found at i:1297241 original size:2 final size:2
Alignment explanation
Indices: 1297234--1297265 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1297224 AATATTTTAA
1297234 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
1297266 TATTTCGGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1302415 original size:231 final size:231
Alignment explanation
Indices: 1302011--1302474 Score: 820
Period size: 231 Copynumber: 2.0 Consensus size: 231
1302001 AGTTAAGTTT
*
1302011 TAAGGGTTGAAATGACTTAAAGGTATGGAGTTTATATAAGTTTTGATAAATTTTCGGGTTAAAAC
1 TAAGGGTTGAAAGGACTTAAAGGTATGGAGTTTATATAAGTTTTGATAAATTTTCGGGTTAAAAC
*
1302076 AAGTAAGTTATGGGCAAGAGGTATCGGTACTGGGTGAACAATACCAACACTTAAAGGCAAAAATA
66 AAGTAAGTTATGGGCAAGAGGTATCGGTACTGGATGAACAATACCAACACTTAAAGGCAAAAATA
* *
1302141 AGTGATGTCTTGGTATGGGTATCGATACTGGATGAACAATATCGATACCTTAAGGTAGAAGTGGA
131 AGTGATATCTTGGTATGGGTATCGAAACTGGATGAACAATATCGATACCTTAAGGTAGAAGTGGA
1302206 TGAATTCTTCAAAGAGTATCGATACCAAAGTAGTAG
196 TGAATTCTTCAAAGAGTATCGATACCAAAGTAGTAG
* *
1302242 TAAGGGTTGAAAGGACTTAAAGGTATGGAGTTTATATAAGTTTTGGTAAATTTTCGGGTTAAAAT
1 TAAGGGTTGAAAGGACTTAAAGGTATGGAGTTTATATAAGTTTTGATAAATTTTCGGGTTAAAAC
* *
1302307 GAGTAAGTTATGGGCAAGAGGTATCGGTACTGGATGAACAGTACCAACACTTAAAGGCAAAAATA
66 AAGTAAGTTATGGGCAAGAGGTATCGGTACTGGATGAACAATACCAACACTTAAAGGCAAAAATA
* * *
1302372 GGTGATATCTTGGTCTGGGTATCGAAACTGGATGAATAATATCGATACCTTAAGGTAGAAGTGGA
131 AGTGATATCTTGGTATGGGTATCGAAACTGGATGAACAATATCGATACCTTAAGGTAGAAGTGGA
*
1302437 TGAATTCTTCAAAGAGTATCGATATCAAAGTAGTAG
196 TGAATTCTTCAAAGAGTATCGATACCAAAGTAGTAG
1302473 TA
1 TA
1302475 TCGATACTAA
Statistics
Matches: 221, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
231 221 1.00
ACGTcount: A:0.36, C:0.10, G:0.25, T:0.29
Consensus pattern (231 bp):
TAAGGGTTGAAAGGACTTAAAGGTATGGAGTTTATATAAGTTTTGATAAATTTTCGGGTTAAAAC
AAGTAAGTTATGGGCAAGAGGTATCGGTACTGGATGAACAATACCAACACTTAAAGGCAAAAATA
AGTGATATCTTGGTATGGGTATCGAAACTGGATGAACAATATCGATACCTTAAGGTAGAAGTGGA
TGAATTCTTCAAAGAGTATCGATACCAAAGTAGTAG
Found at i:1303360 original size:23 final size:23
Alignment explanation
Indices: 1303334--1303417 Score: 87
Period size: 23 Copynumber: 3.7 Consensus size: 23
1303324 AAGTAGAGGG
* *
1303334 TTCTACGCGGTCATTTGGGGCAA
1 TTCTACGCGGTCCTTTGGGACAA
* * *
1303357 TTCTACGTGGTCCTTCGGGACAT
1 TTCTACGCGGTCCTTTGGGACAA
*
1303380 TTCTACGCGATCCTTTGGGACAA
1 TTCTACGCGGTCCTTTGGGACAA
* * *
1303403 TACTATGAGGTCCTT
1 TTCTACGCGGTCCTT
1303418 CAGGACATTT
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.33
Consensus pattern (23 bp):
TTCTACGCGGTCCTTTGGGACAA
Found at i:1303415 original size:46 final size:46
Alignment explanation
Indices: 1303334--1303430 Score: 131
Period size: 46 Copynumber: 2.1 Consensus size: 46
1303324 AAGTAGAGGG
* * * * *
1303334 TTCTACGCGGTCATTTGGGGCAATTCTACGTGGTCCTTCGGGACAT
1 TTCTACGCGATCATTTGGGACAATACTACGAGGTCCTTCAGGACAT
* *
1303380 TTCTACGCGATCCTTTGGGACAATACTATGAGGTCCTTCAGGACAT
1 TTCTACGCGATCATTTGGGACAATACTACGAGGTCCTTCAGGACAT
1303426 TTCTA
1 TTCTA
1303431 TGTGGCACTT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.33
Consensus pattern (46 bp):
TTCTACGCGATCATTTGGGACAATACTACGAGGTCCTTCAGGACAT
Found at i:1303431 original size:23 final size:23
Alignment explanation
Indices: 1303365--1303432 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
1303355 AATTCTACGT
* *
1303365 GGTCCTTCGGGACATTTCTACGC
1 GGTCCTTCGGGACATTTCTATGA
* * * *
1303388 GATCCTTTGGGACAATACTATGA
1 GGTCCTTCGGGACATTTCTATGA
*
1303411 GGTCCTTCAGGACATTTCTATG
1 GGTCCTTCGGGACATTTCTATG
1303433 TGGCACTTCG
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.32
Consensus pattern (23 bp):
GGTCCTTCGGGACATTTCTATGA
Found at i:1303634 original size:31 final size:31
Alignment explanation
Indices: 1303599--1303658 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
1303589 TGTTGATAAT
*
1303599 GATGATGAGAACAAATGTTGATAATGATATC
1 GATGATGAGAACAAATATTGATAATGATATC
*
1303630 GATGATGAGAACATATATTGATAATGATA
1 GATGATGAGAACAAATATTGATAATGATA
1303659 ATGATGTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.22, T:0.30
Consensus pattern (31 bp):
GATGATGAGAACAAATATTGATAATGATATC
Done.