Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007905.1 Hibiscus syriacus cultivar Beakdansim tig00110299_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: 2946335
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 14
Found at i:1232400 original size:21 final size:21
Alignment explanation
Indices: 1232346--1232410 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
1232336 GTCTTTGGTT
1232346 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
1232367 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
1232387 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
1232408 GAA
1 GAA
1232411 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:1232471 original size:14 final size:14
Alignment explanation
Indices: 1232452--1232508 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1232442 TTTGGTTTCG
1232452 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1232466 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1232485 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1232499 CGTTGCGATT
1 CGTTGCGATT
1232509 TTCATTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1232484 original size:33 final size:33
Alignment explanation
Indices: 1232436--1232515 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
1232426 AAAATCGCAA
**
1232436 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1232469 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1232502 TGCGATTTTCATTT
1 TGCGATTTTCATTT
1232516 TTCTCGTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1232521 original size:21 final size:21
Alignment explanation
Indices: 1232496--1232569 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
1232486 GTTGCGATTC
1232496 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
1232517 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
1232538 TCACGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTT
1232559 TCTCGTTGCGA
1 TCTCGTTGCGA
1232570 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.73
22 6 0.14
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:1232691 original size:33 final size:33
Alignment explanation
Indices: 1232649--1232719 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1232639 AATACTAACT
1232649 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
1232682 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1232715 TGAAA
1 TGAAA
1232720 TCTAAGTGAA
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:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:1233124 original size:20 final size:20
Alignment explanation
Indices: 1233099--1233291 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
1233089 CTTTAAAAAT
1233099 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1233119 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
1233139 TGTCGTTGCAATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
1233160 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1233180 TGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1233200 CGTGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1233220 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1233240 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1233260 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1233280 CGCGTTGCGATT
1 CGCGTTGCGATT
1233292 CTGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
20 129 0.88
21 17 0.12
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1234154 original size:24 final size:24
Alignment explanation
Indices: 1234122--1234168 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1234112 ATGTATTACA
1234122 TTATATTTACTCTAGATTTATAAT
1 TTATATTTACTCTAGATTTATAAT
*
1234146 TTATATTTACTCTATATTTATAA
1 TTATATTTACTCTAGATTTATAA
1234169 AAATACGTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.09, G:0.02, T:0.55
Consensus pattern (24 bp):
TTATATTTACTCTAGATTTATAAT
Found at i:1242520 original size:20 final size:20
Alignment explanation
Indices: 1242495--1242544 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1242485 TTACCTTGGG
*
1242495 TATCGATACTACAAGAACAT
1 TATCGATACTACAAGAACAA
**
1242515 TATCGATACTGTAAGAACAA
1 TATCGATACTACAAGAACAA
*
1242535 TATCAATACT
1 TATCGATACT
1242545 TCTTATCCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (20 bp):
TATCGATACTACAAGAACAA
Found at i:1245767 original size:15 final size:15
Alignment explanation
Indices: 1245747--1245781 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1245737 AGGGTTTGTA
*
1245747 CTTTATAAAGCTCCT
1 CTTTATAAAACTCCT
1245762 CTTTATAAAACTCCT
1 CTTTATAAAACTCCT
1245777 CTTTA
1 CTTTA
1245782 CGGGGAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.26, G:0.03, T:0.43
Consensus pattern (15 bp):
CTTTATAAAACTCCT
Found at i:1246725 original size:25 final size:26
Alignment explanation
Indices: 1246688--1246748 Score: 99
Period size: 25 Copynumber: 2.4 Consensus size: 26
1246678 CGTGTTGAGG
1246688 TAAGT-TTATACTAGTGAAGTC-TCT
1 TAAGTCTTATACTAGTGAAGTCTTCT
*
1246712 TAAGTCTTGTACTAGTGAAGTCTTCT
1 TAAGTCTTATACTAGTGAAGTCTTCT
1246738 TAAGTCTTATA
1 TAAGTCTTATA
1246749 GAATTAACAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
24 5 0.15
25 15 0.45
26 13 0.39
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.43
Consensus pattern (26 bp):
TAAGTCTTATACTAGTGAAGTCTTCT
Found at i:1247483 original size:35 final size:35
Alignment explanation
Indices: 1247418--1247490 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 35
1247408 CGTTATAGAA
* * * * *
1247418 CTAAACTTTTTGCGGTGTTTGTATATAAAACGGCG
1 CTAAACCTGTTGCGGTGTTTGAATACAAAACGCCG
*
1247453 CTAAACCTGTTGCGGTGTTTGAATCCAAAACGCCG
1 CTAAACCTGTTGCGGTGTTTGAATACAAAACGCCG
1247488 CTA
1 CTA
1247491 TAGATCTCGA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.32
Consensus pattern (35 bp):
CTAAACCTGTTGCGGTGTTTGAATACAAAACGCCG
Found at i:1255005 original size:3 final size:3
Alignment explanation
Indices: 1254999--1255042 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
1254989 AGAAATAATG
*
1254999 GAA GAA GAA GAA GAA TAA GAA G-A GAA -AA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1255043 CCATGGACTC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 4 0.11
3 33 0.89
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:1255100 original size:33 final size:33
Alignment explanation
Indices: 1255053--1255118 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1255043 CCATGGACTC
*
1255053 TATTATTCTGAAGAAGAAGAAAACACCCGAATG
1 TATTATTCTAAAGAAGAAGAAAACACCCGAATG
* *
1255086 TATTATTCTAAAGAAGAAGAAGACACTCGAATG
1 TATTATTCTAAAGAAGAAGAAAACACCCGAATG
1255119 CCAACTCACC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.23
Consensus pattern (33 bp):
TATTATTCTAAAGAAGAAGAAAACACCCGAATG
Found at i:1256739 original size:29 final size:29
Alignment explanation
Indices: 1256707--1256855 Score: 97
Period size: 29 Copynumber: 5.2 Consensus size: 29
1256697 AATTAATTCG
*
1256707 AAAAGGGTGCTATTTTTGTAATTTTTTTA
1 AAAAAGGTGCTATTTTTGTAATTTTTTTA
** * *
1256736 AAAAAAATGCTATTTTCGTATTTTTTTTGA
1 AAAAAGGTGCTATTTTTGTAATTTTTTT-A
* * * * * *
1256766 AAAAAAG-AC-ATTTTAGTAAATATTTTG
1 AAAAAGGTGCTATTTTTGTAATTTTTTTA
* * * *
1256793 AAAATGGTGCTATATTGGTAATTAATTTT-
1 AAAAAGGTGCTATTTTTGTAATT-TTTTTA
* * *
1256822 AAAATGGTGCTATTTTTGTAATTTTGTAA
1 AAAAAGGTGCTATTTTTGTAATTTTTTTA
1256851 AAAAA
1 AAAAA
1256856 TAATAATTTC
Statistics
Matches: 91, Mismatches: 24, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
27 5 0.05
28 16 0.18
29 58 0.64
30 12 0.13
ACGTcount: A:0.37, C:0.04, G:0.14, T:0.45
Consensus pattern (29 bp):
AAAAAGGTGCTATTTTTGTAATTTTTTTA
Found at i:1262046 original size:211 final size:211
Alignment explanation
Indices: 1261682--1262105 Score: 794
Period size: 211 Copynumber: 2.0 Consensus size: 211
1261672 GAAGATTGAG
*
1261682 CAGAAAAGATCAACTCTTTGATCGGATGTTTATTCGTGGTACAATTGAGTTGATATTTAGACAAC
1 CAGAAAAGATCAACTCTTTGATCGAATGTTTATTCGTGGTACAATTGAGTTGATATTTAGACAAC
* *
1261747 AATTAGACAATTTTAAGTTATTGACTTTGTACGATCGAATTTTCATTCTATTCCTATAGTTTTCC
66 AATTAGACAATTTTAAGTTATTGACTTTGTACGATCGAATTTTCATTCGATTCCTATAGCTTTCC
1261812 ACACCTACGACTGTTTAACAATCATAAACTTGACTAAAATAAACTTTTAATTACAATTGAGAGAT
131 ACACCTACGACTGTTTAACAATCATAAACTTGACTAAAATAAACTTTTAATTACAATTGAGAGAT
1261877 CAAATGAATTATTATT
196 CAAATGAATTATTATT
1261893 CAGAAAAGATCAACTCTTTGATCGAATGTTTATTCGTGGTACAATTGAGTTGATATTTAGACAAC
1 CAGAAAAGATCAACTCTTTGATCGAATGTTTATTCGTGGTACAATTGAGTTGATATTTAGACAAC
* *
1261958 AGTTAGACAATTTTAAGTTATTGACTTTGTACGATCGAATTTTCATTCGATTCCTGTAGCTTTCC
66 AATTAGACAATTTTAAGTTATTGACTTTGTACGATCGAATTTTCATTCGATTCCTATAGCTTTCC
*
1262023 ACACCTACGACTGTTTAACAATCATAAACTTGACTAAAATAAACTTTTAATTACAATTGAGGGAT
131 ACACCTACGACTGTTTAACAATCATAAACTTGACTAAAATAAACTTTTAATTACAATTGAGAGAT
1262088 CAAATGAATTATTATT
196 CAAATGAATTATTATT
1262104 CA
1 CA
1262106 TTAATTGTTA
Statistics
Matches: 207, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
211 207 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (211 bp):
CAGAAAAGATCAACTCTTTGATCGAATGTTTATTCGTGGTACAATTGAGTTGATATTTAGACAAC
AATTAGACAATTTTAAGTTATTGACTTTGTACGATCGAATTTTCATTCGATTCCTATAGCTTTCC
ACACCTACGACTGTTTAACAATCATAAACTTGACTAAAATAAACTTTTAATTACAATTGAGAGAT
CAAATGAATTATTATT
Found at i:1262209 original size:11 final size:11
Alignment explanation
Indices: 1262195--1262230 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
1262185 TTTATATTAT
1262195 ATTTTTATTTC
1 ATTTTTATTTC
*
1262206 ATTTTTATTGC
1 ATTTTTATTTC
1262217 ATTTTTATTT-
1 ATTTTTATTTC
1262227 ATTT
1 ATTT
1262231 ATTTAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 4 0.17
11 19 0.83
ACGTcount: A:0.19, C:0.06, G:0.03, T:0.72
Consensus pattern (11 bp):
ATTTTTATTTC
Found at i:1263538 original size:3 final size:3
Alignment explanation
Indices: 1263530--1263575 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
1263520 ATCGAATAAG
1263530 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1263576 ATTTCTTTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1265047 original size:26 final size:26
Alignment explanation
Indices: 1265017--1265066 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
1265007 ACATCTAAAA
1265017 TAAGTCGTATGTTATATAGTACTTCT
1 TAAGTCGTATGTTATATAGTACTTCT
1265043 TAAGTCGTATGTTATATAGTACTT
1 TAAGTCGTATGTTATATAGTACTT
1265067 GCTTTGATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.28, C:0.10, G:0.16, T:0.46
Consensus pattern (26 bp):
TAAGTCGTATGTTATATAGTACTTCT
Found at i:1267569 original size:6 final size:6
Alignment explanation
Indices: 1267558--1267628 Score: 142
Period size: 6 Copynumber: 11.8 Consensus size: 6
1267548 AGCTTCACCG
1267558 TTACCA TTACCA TTACCA TTACCA TTACCA TTACCA TTACCA TTACCA
1 TTACCA TTACCA TTACCA TTACCA TTACCA TTACCA TTACCA TTACCA
1267606 TTACCA TTACCA TTACCA TTACC
1 TTACCA TTACCA TTACCA TTACC
1267629 GTCTTCTTCG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 65 1.00
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (6 bp):
TTACCA
Found at i:1269364 original size:20 final size:20
Alignment explanation
Indices: 1269322--1269365 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1269312 TTGTGGACTA
* **
1269322 TCAAATCAACACCGTGATTG
1 TCAAATCAACACCGTAACAG
*
1269342 TCAAATCAATACCGTAACAG
1 TCAAATCAACACCGTAACAG
1269362 TCAA
1 TCAA
1269366 CGACGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.25, G:0.11, T:0.23
Consensus pattern (20 bp):
TCAAATCAACACCGTAACAG
Found at i:1269540 original size:68 final size:68
Alignment explanation
Indices: 1269431--1269573 Score: 277
Period size: 68 Copynumber: 2.1 Consensus size: 68
1269421 ACCACGTTAA
1269431 AAAAATAAATAATAAGATTACTCCTATTATTTTTTTACGTACAGGGGCGTCTTATACCTTTTTGC
1 AAAAA-AAATAATAAGATTACTCCTATTATTTTTTTACGTACAGGGGCGTCTTATACCTTTTTGC
1269496 TAAT
65 TAAT
1269500 AAAAAAAATAATAAGATTACTCCTATTATTTTTTTACGTACAGGGGCGTCTTATACCTTTTTGCT
1 AAAAAAAATAATAAGATTACTCCTATTATTTTTTTACGTACAGGGGCGTCTTATACCTTTTTGCT
1269565 AAT
66 AAT
1269568 AAAAAA
1 AAAAAA
1269574 GGAAAACTGA
Statistics
Matches: 74, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
68 69 0.93
69 5 0.07
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.38
Consensus pattern (68 bp):
AAAAAAAATAATAAGATTACTCCTATTATTTTTTTACGTACAGGGGCGTCTTATACCTTTTTGCT
AAT
Found at i:1270243 original size:18 final size:19
Alignment explanation
Indices: 1270185--1270242 Score: 93
Period size: 18 Copynumber: 3.2 Consensus size: 19
1270175 ATTCCTGTGT
1270185 CCCCTTT-CCCTTTCTCTC
1 CCCCTTTCCCCTTTCTCTC
1270203 CCCCTTTCCCC-TTCTCTC
1 CCCCTTTCCCCTTTCTCTC
*
1270221 CCCCTTTCCCCTTTCACTC
1 CCCCTTTCCCCTTTCTCTC
1270240 CCC
1 CCC
1270243 TGCTCGGTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
18 25 0.68
19 12 0.32
ACGTcount: A:0.02, C:0.60, G:0.00, T:0.38
Consensus pattern (19 bp):
CCCCTTTCCCCTTTCTCTC
Found at i:1275105 original size:16 final size:17
Alignment explanation
Indices: 1275072--1275105 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1275062 CCTTTTATTT
*
1275072 TTATTTTATATTTTAAA
1 TTATTTTATATATTAAA
1275089 TTATTTT-TATATTAAA
1 TTATTTTATATATTAAA
1275105 T
1 T
1275106 AATAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTTTATATATTAAA
Found at i:1279311 original size:17 final size:19
Alignment explanation
Indices: 1279291--1279330 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
1279281 TTTTATGAGA
1279291 ATGATTGGAAA-A-TGATT
1 ATGATTGGAAATATTGATT
*
1279308 ATGATTTGAAATATTGATT
1 ATGATTGGAAATATTGATT
1279327 ATGA
1 ATGA
1279331 AACGAACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 10 0.50
18 1 0.05
19 9 0.45
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (19 bp):
ATGATTGGAAATATTGATT
Found at i:1279763 original size:19 final size:19
Alignment explanation
Indices: 1279736--1279815 Score: 151
Period size: 19 Copynumber: 4.2 Consensus size: 19
1279726 TTGTGTACCA
*
1279736 ATGCACATGCCATGCATCG
1 ATGCGCATGCCATGCATCG
1279755 ATGCGCATGCCATGCATCG
1 ATGCGCATGCCATGCATCG
1279774 ATGCGCATGCCATGCATCG
1 ATGCGCATGCCATGCATCG
1279793 ATGCGCATGCCATGCATCG
1 ATGCGCATGCCATGCATCG
1279812 ATGC
1 ATGC
1279816 AATCCTGGCT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 60 1.00
ACGTcount: A:0.23, C:0.31, G:0.25, T:0.21
Consensus pattern (19 bp):
ATGCGCATGCCATGCATCG
Found at i:1281807 original size:21 final size:21
Alignment explanation
Indices: 1281783--1281822 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1281773 AAGACTTTAT
1281783 TTTCAAAATAT-AAAAATGATA
1 TTTCAAAAT-TGAAAAATGATA
1281804 TTTCAAAATTGAAAAATGA
1 TTTCAAAATTGAAAAATGA
1281823 AAATAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (21 bp):
TTTCAAAATTGAAAAATGATA
Found at i:1282246 original size:30 final size:30
Alignment explanation
Indices: 1282210--1282270 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
1282200 ATGAATATGG
1282210 ACCCAAAAGAAATTGGGTACCAAAAATCAA
1 ACCCAAAAGAAATTGGGTACCAAAAATCAA
1282240 ACCCAAAAGAAATTGGGTACCAAAAATCAA
1 ACCCAAAAGAAATTGGGTACCAAAAATCAA
1282270 A
1 A
1282271 TTTTAATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.54, C:0.20, G:0.13, T:0.13
Consensus pattern (30 bp):
ACCCAAAAGAAATTGGGTACCAAAAATCAA
Found at i:1285259 original size:15 final size:15
Alignment explanation
Indices: 1285239--1285272 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1285229 GTACATTGAA
*
1285239 ATTAGACATCATTTC
1 ATTAGACATCATGTC
*
1285254 ATTAGAGATCATGTC
1 ATTAGACATCATGTC
1285269 ATTA
1 ATTA
1285273 AAGAAGATAT
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:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (15 bp):
ATTAGACATCATGTC
Found at i:1285706 original size:23 final size:22
Alignment explanation
Indices: 1285680--1285753 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 22
1285670 GAGTGTGTAC
1285680 CGATGCATCCCTTGAATGTGCAT
1 CGATGCAT-CCTTGAATGTGCAT
* * * *
1285703 CGATACA-CCATGAAGGTGCAC
1 CGATGCATCCTTGAATGTGCAT
* **
1285724 CAATTTATTCCTTGAATGTGCAT
1 CGATGCA-TCCTTGAATGTGCAT
1285747 CGATGCA
1 CGATGCA
1285754 CTCTGCTGTG
Statistics
Matches: 36, Mismatches: 13, Indels: 4
0.68 0.25 0.08
Matches are distributed among these distances:
21 15 0.42
23 21 0.58
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.28
Consensus pattern (22 bp):
CGATGCATCCTTGAATGTGCAT
Found at i:1288465 original size:65 final size:65
Alignment explanation
Indices: 1288395--1288548 Score: 204
Period size: 65 Copynumber: 2.4 Consensus size: 65
1288385 CACACCCATT
*
1288395 TCGAATGCATTTTGTGTACCGATGCACAAGCCATGCATCGATGCACT-CTTGAATAT-TTTGAAA
1 TCGAATGCATTTTGTGTACCGATGCACAAGACATGCATCGATGCACTAC-TGAAT-TGTTTGAAA
1288458 CA
64 CA
* * * *
1288460 TCGAATGCATTTTATGTACCGATGCACATGATATGCATCGATGCACTACTGACTTGTTTGAAACA
1 TCGAATGCATTTTGTGTACCGATGCACAAGACATGCATCGATGCACTACTGAATTGTTTGAAACA
* * *
1288525 TCGAATGTAATTAGTGTACCGATG
1 TCGAATGCATTTTGTGTACCGATG
1288549 TACTCCTAGT
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
64 1 0.01
65 76 0.97
66 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Consensus pattern (65 bp):
TCGAATGCATTTTGTGTACCGATGCACAAGACATGCATCGATGCACTACTGAATTGTTTGAAACA
Found at i:1292642 original size:22 final size:22
Alignment explanation
Indices: 1292611--1292685 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
1292601 ATTAAGGGTA
1292611 GTATCAATACTAGTTGAAGAGG
1 GTATCAATACTAGTTGAAGAGG
* * *
1292633 GTATCGATACTA--TGTAG-GTA
1 GTATCAATACTAGTTGAAGAG-G
1292653 GTATCAATACTAGTTGAAGAGG
1 GTATCAATACTAGTTGAAGAGG
* *
1292675 CTATCTATACT
1 GTATCAATACT
1292686 GTGTGGGTAG
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
19 1 0.02
20 15 0.37
22 24 0.59
23 1 0.02
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.32
Consensus pattern (22 bp):
GTATCAATACTAGTTGAAGAGG
Found at i:1292654 original size:42 final size:42
Alignment explanation
Indices: 1292607--1292704 Score: 151
Period size: 42 Copynumber: 2.3 Consensus size: 42
1292597 AATTATTAAG
*
1292607 GGTAGTATCAATACTAGTTGAAGAGGGTATCGATACTATGTA
1 GGTAGTATCAATACTAGTTGAAGAGGCTATCGATACTATGTA
* * *
1292649 GGTAGTATCAATACTAGTTGAAGAGGCTATCTATACTGTGTG
1 GGTAGTATCAATACTAGTTGAAGAGGCTATCGATACTATGTA
*
1292691 GGTAGTATCGATAC
1 GGTAGTATCAATAC
1292705 CAGGGGGATG
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.31, C:0.11, G:0.27, T:0.32
Consensus pattern (42 bp):
GGTAGTATCAATACTAGTTGAAGAGGCTATCGATACTATGTA
Found at i:1293378 original size:21 final size:21
Alignment explanation
Indices: 1293349--1293406 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
1293339 GTCAAAGGTT
*
1293349 TTATGTGGTCATTCGGGACAA
1 TTATATGGTCATTCGGGACAA
*
1293370 TTATATGGTCATTCAGGACAA
1 TTATATGGTCATTCGGGACAA
*
1293391 ATATATGG-CACTTCGG
1 TTATATGGTCA-TTCGG
1293407 TGCAAACCTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 2 0.06
21 30 0.94
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.33
Consensus pattern (21 bp):
TTATATGGTCATTCGGGACAA
Found at i:1293412 original size:21 final size:22
Alignment explanation
Indices: 1293388--1293436 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 22
1293378 TCATTCAGGA
1293388 CAAA-TATATGGCACTTCGGTG
1 CAAACTATATGGCACTTCGGTG
*
1293409 CAAACCTATGTGGCACTTCGGTG
1 CAAA-CTATATGGCACTTCGGTG
1293432 CAAAC
1 CAAAC
1293437 CTATTTGGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 4 0.16
22 1 0.04
23 20 0.80
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (22 bp):
CAAACTATATGGCACTTCGGTG
Found at i:1293450 original size:23 final size:23
Alignment explanation
Indices: 1293396--1293440 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
1293386 GACAAATATA
1293396 TGGCACTTCGGTGCAAACCTATG
1 TGGCACTTCGGTGCAAACCTATG
1293419 TGGCACTTCGGTGCAAACCTAT
1 TGGCACTTCGGTGCAAACCTAT
1293441 TTGGTCCTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (23 bp):
TGGCACTTCGGTGCAAACCTATG
Found at i:1299604 original size:22 final size:21
Alignment explanation
Indices: 1299579--1299653 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 21
1299569 ATTAAGGGTA
1299579 GTATCGATACTAGTTAAAGAGG
1 GTATCGATACTAGTT-AAGAGG
* *
1299601 GTATCGATA-TTGTGT-AG-GTA
1 GTATCGATACTAGT-TAAGAG-G
*
1299621 GTATCGATACCAGTTGAAGAGG
1 GTATCGATACTAGTT-AAGAGG
1299643 GTATCGATACT
1 GTATCGATACT
1299654 TTATGGGTAG
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
19 1 0.02
20 12 0.29
21 5 0.12
22 22 0.54
23 1 0.02
ACGTcount: A:0.31, C:0.11, G:0.28, T:0.31
Consensus pattern (21 bp):
GTATCGATACTAGTTAAGAGG
Found at i:1299623 original size:42 final size:42
Alignment explanation
Indices: 1299575--1299675 Score: 150
Period size: 42 Copynumber: 2.4 Consensus size: 42
1299565 AATTATTAAG
* *
1299575 GGTAGTATCGATACTAGTTAAAGAGGGTATCGATA-TTGTGTA
1 GGTAGTATCGATACCAGTTAAAGAGGGTATCGATACTT-TATA
* *
1299617 GGTAGTATCGATACCAGTTGAAGAGGGTATCGATACTTTATG
1 GGTAGTATCGATACCAGTTAAAGAGGGTATCGATACTTTATA
1299659 GGTAGTATCGATACCAG
1 GGTAGTATCGATACCAG
1299676 GGGATGGTAT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
42 52 0.96
43 2 0.04
ACGTcount: A:0.30, C:0.11, G:0.29, T:0.31
Consensus pattern (42 bp):
GGTAGTATCGATACCAGTTAAAGAGGGTATCGATACTTTATA
Found at i:1300357 original size:21 final size:21
Alignment explanation
Indices: 1300318--1300359 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1300308 GTCAAAGGTT
*
1300318 TTATGTGATCCTGTGGGACAA
1 TTATGTGATCCTGTAGGACAA
1300339 TTATGTGATCCT-TCAGGACAA
1 TTATGTGATCCTGT-AGGACAA
1300360 ATATATGGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (21 bp):
TTATGTGATCCTGTAGGACAA
Found at i:1300395 original size:23 final size:22
Alignment explanation
Indices: 1300357--1300448 Score: 75
Period size: 23 Copynumber: 4.2 Consensus size: 22
1300347 TCCTTCAGGA
*
1300357 CAAA-TATATGGCACTTCGGTG
1 CAAACTATGTGGCACTTCGGTG
1300378 CAAAGCTATGTGGCACTTCGGTG
1 CAAA-CTATGTGGCACTTCGGTG
* * *
1300401 AAAACCTATTTGGTCA-TTTGG-G
1 CAAA-CTATGTGG-CACTTCGGTG
*
1300423 -ATAATTATGTGGCACTTCGGTG
1 CA-AACTATGTGGCACTTCGGTG
1300445 CAAA
1 CAAA
1300449 TTACAAGCTG
Statistics
Matches: 56, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
20 2 0.04
21 15 0.27
22 6 0.11
23 31 0.55
24 2 0.04
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (22 bp):
CAAACTATGTGGCACTTCGGTG
Found at i:1301176 original size:18 final size:18
Alignment explanation
Indices: 1301139--1301179 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1301129 CTATTGAGCC
* *
1301139 TGAAATTGTAAGATAGAT
1 TGAAATTGTAAGAGAAAT
*
1301157 TGAAATTGTAATAGAAAT
1 TGAAATTGTAAGAGAAAT
1301175 TGAAA
1 TGAAA
1301180 ATAATACTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.20, T:0.32
Consensus pattern (18 bp):
TGAAATTGTAAGAGAAAT
Found at i:1301647 original size:46 final size:46
Alignment explanation
Indices: 1301566--1301924 Score: 497
Period size: 46 Copynumber: 7.8 Consensus size: 46
1301556 TAACTACATA
* *
1301566 AAAGGATGCCATAAAT-AAAATCCATAACGATGCATTATCGGCATG
1 AAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGCATG
*
1301611 AAAGGATGCCATAAATGAAAATGCATAAGGGTGCATTATCAGG-ATG
1 AAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATC-GGCATG
**
1301657 AAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGAAATG
1 AAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGCATG
* * * * *
1301703 AAAGGATGCCATAAATGAAAATGCATAATGATACATTATTGGCATA
1 AAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGCATG
* *
1301749 AAAGGATGCCATAAATGAAAATGCATAACAGTGCATTATCGACATG
1 AAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGCATG
* ** * *
1301795 AAAGGATGCCAGAAATGAAAATATATAATGGTGCATTATCAGCATG
1 AAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGCATG
*
1301841 AAAGGATGCAATAAATGAAAATGCATAACGGTGCATTATCGGCATG
1 AAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGCATG
* * * *
1301887 AAATGATGCCACAAATGAAAATACATAACGGTGTATTA
1 AAAGGATGCCATAAATGAAAATGCATAACGGTGCATTA
1301925 ACGACATAAA
Statistics
Matches: 274, Mismatches: 37, Indels: 5
0.87 0.12 0.02
Matches are distributed among these distances:
45 17 0.06
46 255 0.93
47 2 0.01
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.23
Consensus pattern (46 bp):
AAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCGGCATG
Found at i:1301937 original size:92 final size:91
Alignment explanation
Indices: 1301537--1301937 Score: 498
Period size: 92 Copynumber: 4.4 Consensus size: 91
1301527 ATGAATGAAT
* * * * *
1301537 AAAATACATAACGATGTATTAACTACATAAAAGGATGCCATAAAT-AAAATCCATAACGATGCAT
1 AAAATACATAACGGTGCATTATC-ACATAAAAGGATGCCATAAATGAAAATGCATAACGGTGCAT
*
1301601 TATCGGCATGAAAGGATGCCATAAATG
65 TATCGACATGAAAGGATGCCATAAATG
* * * *
1301628 AAAATGCATAAGGGTGCATTATCAGGATGAAAGGATGCCATAAATGAAAATGCATAACGGTGCAT
1 AAAATACATAACGGTGCATTATCA-CATAAAAGGATGCCATAAATGAAAATGCATAACGGTGCAT
*
1301693 TATCGAAATGAAAGGATGCCATAAATG
65 TATCGACATGAAAGGATGCCATAAATG
* * * * ** *
1301720 AAAATGCATAATGATACATTATTGGCATAAAAGGATGCCATAAATGAAAATGCATAACAGTGCAT
1 AAAATACATAACGGTGCATTA-TCACATAAAAGGATGCCATAAATGAAAATGCATAACGGTGCAT
*
1301785 TATCGACATGAAAGGATGCCAGAAATG
65 TATCGACATGAAAGGATGCCATAAATG
* * * *
1301812 AAAATATATAATGGTGCATTATCAGCATGAAAGGATGCAATAAATGAAAATGCATAACGGTGCAT
1 AAAATACATAACGGTGCATTATCA-CATAAAAGGATGCCATAAATGAAAATGCATAACGGTGCAT
* * *
1301877 TATCGGCATGAAATGATGCCACAAATG
65 TATCGACATGAAAGGATGCCATAAATG
* *
1301904 AAAATACATAACGGTGTATTAACGACATAAAAGG
1 AAAATACATAACGGTGCATTATC-ACATAAAAGG
1301938 TGTCACTCAT
Statistics
Matches: 267, Mismatches: 38, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
90 1 0.00
91 37 0.14
92 227 0.85
93 2 0.01
ACGTcount: A:0.44, C:0.13, G:0.20, T:0.23
Consensus pattern (91 bp):
AAAATACATAACGGTGCATTATCACATAAAAGGATGCCATAAATGAAAATGCATAACGGTGCATT
ATCGACATGAAAGGATGCCATAAATG
Found at i:1312955 original size:25 final size:23
Alignment explanation
Indices: 1312909--1312955 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
1312899 AGGCCAGGTT
* *
1312909 AATTTGTTTAATTCAACTATTAC
1 AATTTGTTTAATCCAACAATTAC
1312932 AATTATGTTTAAATCCAACAATTA
1 AATT-TGTTT-AATCCAACAATTA
1312956 AATCATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 5 0.25
25 11 0.55
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.43
Consensus pattern (23 bp):
AATTTGTTTAATCCAACAATTAC
Found at i:1314523 original size:6 final size:6
Alignment explanation
Indices: 1314514--1314546 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
1314504 TCTCGTGCTC
1314514 GTGGAT GTGGAT GTGGAT GTGGAT GTGGAT GTG
1 GTGGAT GTGGAT GTGGAT GTGGAT GTGGAT GTG
1314547 AAAAAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.00, G:0.52, T:0.33
Consensus pattern (6 bp):
GTGGAT
Found at i:1315422 original size:21 final size:23
Alignment explanation
Indices: 1315375--1315422 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 23
1315365 ATTAAGATAA
* *
1315375 ATTTGAAAATTCCTAGAAATTAT
1 ATTTGAAAATTCCTAGAAAATAG
*
1315398 ATTTG-AAATT-CTTGAAAATAG
1 ATTTGAAAATTCCTAGAAAATAG
1315419 ATTT
1 ATTT
1315423 TAATATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 12 0.55
22 5 0.23
23 5 0.23
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (23 bp):
ATTTGAAAATTCCTAGAAAATAG
Found at i:1315484 original size:31 final size:29
Alignment explanation
Indices: 1315437--1315529 Score: 79
Period size: 31 Copynumber: 3.2 Consensus size: 29
1315427 ATATATATTC
*
1315437 TAAATCAAATAAATAAATAATAAAATTTA
1 TAAATCAAATAAATAAATAAAAAAATTTA
*
1315466 TAAATCAAAATTACATAAATAAAAAAA--TA
1 TAAATC-AAA-TAAATAAATAAAAAAATTTA
*
1315495 -AAA--AAATAAAAAAAATAAAACTAAATTTA
1 TAAATCAAAT-AAATAAATAAAA--AAATTTA
1315524 TAAATC
1 TAAATC
1315530 GTTGTATATA
Statistics
Matches: 50, Mismatches: 4, Indels: 17
0.70 0.06 0.24
Matches are distributed among these distances:
24 1 0.02
25 13 0.26
27 3 0.06
28 3 0.06
29 10 0.20
30 6 0.12
31 14 0.28
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (29 bp):
TAAATCAAATAAATAAATAAAAAAATTTA
Found at i:1315501 original size:16 final size:17
Alignment explanation
Indices: 1315482--1315514 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1315472 AAAATTACAT
1315482 AAAT-AAAAAAATAAAA
1 AAATAAAAAAAATAAAA
1315498 AAATAAAAAAAATAAAA
1 AAATAAAAAAAATAAAA
1315515 CTAAATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (17 bp):
AAATAAAAAAAATAAAA
Found at i:1315505 original size:8 final size:8
Alignment explanation
Indices: 1315482--1315514 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
1315472 AAAATTACAT
1315482 AAATAAAA
1 AAATAAAA
1315490 AAATAAAA
1 AAATAAAA
1315498 AAATAAAAA
1 AAAT-AAAA
1315507 AAATAAAA
1 AAATAAAA
1315515 CTAAATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAATAAAA
Found at i:1316417 original size:12 final size:12
Alignment explanation
Indices: 1316400--1316425 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1316390 ATTTTTATTA
1316400 TTTTAGTAATAT
1 TTTTAGTAATAT
1316412 TTTTAGTAATAT
1 TTTTAGTAATAT
1316424 TT
1 TT
1316426 ATTATTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (12 bp):
TTTTAGTAATAT
Found at i:1317658 original size:3 final size:3
Alignment explanation
Indices: 1317652--1317700 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
1317642 CTTTTTTTGG
* * *
1317652 TAT TAT T-T T-T TAC TAT TAT TAT TAT TAT TAA TAT TAT TTT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1317698 TAT
1 TAT
1317701 CATTTTCAGG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1323687 original size:32 final size:32
Alignment explanation
Indices: 1323651--1323717 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
1323641 ATTTTGATAC
*
1323651 TACATTTATCTGAGACTCCAAAGTCATACCTT
1 TACATTTATCTGAGACACCAAAGTCATACCTT
* * * *
1323683 TACATTTTTTTGAGACACCAAATTCATACTTT
1 TACATTTATCTGAGACACCAAAGTCATACCTT
1323715 TAC
1 TAC
1323718 CTTCTCGGGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.39
Consensus pattern (32 bp):
TACATTTATCTGAGACACCAAAGTCATACCTT
Found at i:1324485 original size:15 final size:14
Alignment explanation
Indices: 1324464--1324614 Score: 73
Period size: 14 Copynumber: 10.4 Consensus size: 14
1324454 AAAAATATAT
1324464 AAAAAGATAGAGAAA
1 AAAAAGATAGA-AAA
*
1324479 TAAAAGATA-AAAA
1 AAAAAGATAGAAAA
1324492 AAAAAGA-AGAAAA
1 AAAAAGATAGAAAA
1324505 AGAAAAGATA-AAATA
1 A-AAAAGATAGAAA-A
* *
1324520 TAGAAAA-AAAGAAGGA
1 -A-AAAAGATAGAA-AA
*
1324536 AAAAAGATAAAAAA
1 AAAAAGATAGAAAA
1324550 GGAGAAAAGATAG-AAA
1 --A-AAAAGATAGAAAA
*
1324566 AAGAAGA-AGAAAA
1 AAAAAGATAGAAAA
*
1324579 AAGATAGA-AGAAAA
1 AA-AAAGATAGAAAA
* *
1324593 AAGAAAAATAAAAAA
1 AA-AAAGATAGAAAA
1324608 GAAAAAG
1 -AAAAAG
1324615 GAGAAAGAAA
Statistics
Matches: 106, Mismatches: 15, Indels: 30
0.70 0.10 0.20
Matches are distributed among these distances:
12 3 0.03
13 24 0.23
14 31 0.29
15 25 0.24
16 15 0.14
17 8 0.08
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (14 bp):
AAAAAGATAGAAAA
Found at i:1324510 original size:27 final size:28
Alignment explanation
Indices: 1324465--1324625 Score: 120
Period size: 27 Copynumber: 5.6 Consensus size: 28
1324455 AAAATATATA
* *
1324465 AAAAGATAGAGAAATAAAAGATAAAAAA-
1 AAAAGA-AGAAAAAGAAAAGATAAAAAAG
1324493 AAAAGAAGAAAAAGAAAAGATAAAATATAG
1 AAAAGAAGAAAAAGAAAAGATAAAA-A-AG
* *
1324523 AAAAAAAGAAGGAA-AAAAGATAAAAAAGGAG
1 AAAAGAAGAA-AAAGAAAAGAT-AAAAA--AG
1324554 AAAAGATAGAAAAAGAAGAAG--AAAAAAG
1 AAAAGA-AGAAAAAGAA-AAGATAAAAAAG
*
1324582 -ATAGAAGAAAAAAGAAAA-ATAAAAAAG
1 AAAAGAAG-AAAAAGAAAAGATAAAAAAG
* *
1324609 AAAA-AGGAGAAAGAAAA
1 AAAAGAAGAAAAAGAAAA
1324626 TAAATCAAGT
Statistics
Matches: 109, Mismatches: 11, Indels: 28
0.74 0.07 0.19
Matches are distributed among these distances:
26 13 0.12
27 38 0.35
28 11 0.10
29 1 0.01
30 22 0.20
31 15 0.14
32 6 0.06
33 3 0.03
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (28 bp):
AAAAGAAGAAAAAGAAAAGATAAAAAAG
Found at i:1324557 original size:17 final size:17
Alignment explanation
Indices: 1324526--1324573 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
1324516 AATATAGAAA
*
1324526 AAAAGAAGGAAAAAAGAT
1 AAAA-AAGGAGAAAAGAT
1324544 AAAAAAGGAGAAAAGAT
1 AAAAAAGGAGAAAAGAT
*
1324561 AGAAAAAGAAGAA
1 A-AAAAAGGAGAA
1324574 GAAAAAAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.73, C:0.00, G:0.23, T:0.04
Consensus pattern (17 bp):
AAAAAAGGAGAAAAGAT
Found at i:1324578 original size:40 final size:42
Alignment explanation
Indices: 1324491--1324616 Score: 129
Period size: 40 Copynumber: 3.0 Consensus size: 42
1324481 AAAGATAAAA
*
1324491 AAAAAAGA-AGAAAAAGAAAAGATAAAATATAGAAAAA-AAGAAGG
1 AAAAAAGATAGAAGAA-AAAAG--AAAA-ATAGAAAAAGAAGAAGG
**
1324535 AAAAAAGATA-AA-AAAGGAGAAAAGATAGAAAAAGAAGAA-G
1 AAAAAAGATAGAAGAAAAAAGAAAA-ATAGAAAAAGAAGAAGG
*
1324575 AAAAAAGATAGAAGAAAAAAGAAAAATA-AAAAAGAAAAAGG
1 AAAAAAGATAGAAGAAAAAAGAAAAATAGAAAAAGAAGAAGG
1324616 A
1 A
1324617 GAAAGAAAAT
Statistics
Matches: 71, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
40 34 0.48
41 12 0.17
42 12 0.17
43 2 0.03
44 10 0.14
45 1 0.01
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (42 bp):
AAAAAAGATAGAAGAAAAAAGAAAAATAGAAAAAGAAGAAGG
Found at i:1324579 original size:13 final size:13
Alignment explanation
Indices: 1324563--1324610 Score: 69
Period size: 13 Copynumber: 3.6 Consensus size: 13
1324553 GAAAAGATAG
1324563 AAAAAGAAGAAGA
1 AAAAAGAAGAAGA
1324576 AAAAAGATAGAAGA
1 AAAAAGA-AGAAGA
* *
1324590 AAAAAGAAAAATA
1 AAAAAGAAGAAGA
1324603 AAAAAGAA
1 AAAAAGAA
1324611 AAAGGAGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
13 19 0.59
14 13 0.41
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (13 bp):
AAAAAGAAGAAGA
Found at i:1324992 original size:21 final size:19
Alignment explanation
Indices: 1324954--1324999 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
1324944 AATTAATCAT
1324954 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
1324974 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
1324995 A-TAAT
1 ACTAAT
1325000 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:1332733 original size:3 final size:3
Alignment explanation
Indices: 1332725--1332756 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1332715 ATGAGCTTTT
*
1332725 AAG AAG AAG AAT AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1332757 AAATAAGAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:1332741 original size:12 final size:12
Alignment explanation
Indices: 1332724--1332765 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
1332714 CATGAGCTTT
1332724 TAAGAAGAAGAA
1 TAAGAAGAAGAA
1332736 TAAGAAGAAGAA
1 TAAGAAGAAGAA
* *
1332748 GAAGAAGAAAAA
1 TAAGAAGAAGAA
1332760 TAAGAA
1 TAAGAA
1332766 CTTTTTGGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.69, C:0.00, G:0.24, T:0.07
Consensus pattern (12 bp):
TAAGAAGAAGAA
Found at i:1334626 original size:20 final size:20
Alignment explanation
Indices: 1334601--1334651 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
1334591 AGCTTTCTCG
1334601 GTATCGATACC-ACCCTACGA
1 GTATCGATACCTACCCTAC-A
*
1334621 GTATCGATACCTTCCCTACA
1 GTATCGATACCTACCCTACA
*
1334641 TTATCGATACC
1 GTATCGATACC
1334652 CATTTCATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 22 0.79
21 6 0.21
ACGTcount: A:0.27, C:0.33, G:0.12, T:0.27
Consensus pattern (20 bp):
GTATCGATACCTACCCTACA
Found at i:1372906 original size:222 final size:221
Alignment explanation
Indices: 1372514--1372960 Score: 806
Period size: 222 Copynumber: 2.0 Consensus size: 221
1372504 AGTTTGAATG
* *
1372514 GATTCTTCAAACTTAGACTGGAACTTAGAATTGGATTTGAACCCTGAACGAAAATGGGTATATAC
1 GATTCTTCAAACCTAGACTGGAACTTAGAATTGGATTTGAACCCTGAACGAAAATGGATATATAC
* *
1372579 TATACTGTTCTTACAGCACCGAAAAAATGCCCTATTTTGAGCTTGAAAAATATTAACTTTCTACC
66 TATACTATTCTTACAGCACCGAAAAAATGCCCTATTTTGAGCTTGAAAAATACTAACTTTCTACC
1372644 CCAAACATTCTACTGAGTGTCCCAATTGTTATTAAAGTCTTATGTATGAACATAGGGGTCATAAA
131 CCAAACATTCTACTGAGTGTCCCAATTGTTATTAAAGTCTTATGTATGAACATAGGGGTCATAAA
1372709 GAGTCTATAAACATGTTAGAAACACT
196 GAGTCTATAAACATGTTAGAAACACT
*
1372735 GATTCTTCAAACCTAGACTGGAACTTAGAATTGGATTTGAACCCTGAACGAAAATGGATATCTAC
1 GATTCTTCAAACCTAGACTGGAACTTAGAATTGGATTTGAACCCTGAACGAAAATGGATATATAC
* *
1372800 TGTACTATTCTTACAGTACCGACAAAAATGCCCTATTTTGAGCTTGAAAAATACTAACTTTCTAC
66 TATACTATTCTTACAGCACCGA-AAAAATGCCCTATTTTGAGCTTGAAAAATACTAACTTTCTA-
1372865 CCCCAAACATTCTACTGAGTG-CCCAATTGTTATTAAAGTCTTATGTATGAACATAGGGGTCATA
129 CCCCAAACATTCTACTGAGTGTCCCAATTGTTATTAAAGTCTTATGTATGAACATAGGGGTCATA
1372929 AAGAGTCTATAAACATGTTAGAAACACT
194 AAGAGTCTATAAACATGTTAGAAACACT
1372957 GATT
1 GATT
1372961 TCTGAATTCT
Statistics
Matches: 217, Mismatches: 7, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
221 81 0.37
222 115 0.53
223 21 0.10
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (221 bp):
GATTCTTCAAACCTAGACTGGAACTTAGAATTGGATTTGAACCCTGAACGAAAATGGATATATAC
TATACTATTCTTACAGCACCGAAAAAATGCCCTATTTTGAGCTTGAAAAATACTAACTTTCTACC
CCAAACATTCTACTGAGTGTCCCAATTGTTATTAAAGTCTTATGTATGAACATAGGGGTCATAAA
GAGTCTATAAACATGTTAGAAACACT
Found at i:1373143 original size:26 final size:26
Alignment explanation
Indices: 1373107--1373164 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
1373097 TAAGAGTGAG
*
1373107 TTTCTCCTTCCCCCTAGCTTTGGAGC
1 TTTCTCATTCCCCCTAGCTTTGGAGC
1373133 TTTCTCATTCCCCCTAGCTTTGGAGC
1 TTTCTCATTCCCCCTAGCTTTGGAGC
1373159 TTTCTC
1 TTTCTC
1373165 CAACTTCTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.09, C:0.36, G:0.14, T:0.41
Consensus pattern (26 bp):
TTTCTCATTCCCCCTAGCTTTGGAGC
Found at i:1380180 original size:103 final size:103
Alignment explanation
Indices: 1380001--1380207 Score: 342
Period size: 103 Copynumber: 2.0 Consensus size: 103
1379991 GATGATTTCC
* *
1380001 TGGTTGATAACAATATTTTCAGTGATAAAGCGGCCCAGAATGAAGCTTGTTTGGTTCGGAGAAAC
1 TGGTTGATAACAATATTTTCAGTGATAAAGCGGCCCAAAATGAAGCTTGTTTGGTTCAGAGAAAC
* *
1380066 AAGAAGCGGGATGAAGTTTTGGAGTCGACGAACAATGA
66 AAGAAGCGGGATGAAGCTCTGGAGTCGACGAACAATGA
* *
1380104 TGGTTGATAACAATATTTTCAGTGATAGAGTGGCCCAAAATGAAGCTTGTTTGGTTCAGAGAAAC
1 TGGTTGATAACAATATTTTCAGTGATAAAGCGGCCCAAAATGAAGCTTGTTTGGTTCAGAGAAAC
* *
1380169 AAGGAGCGGGATGATGCTCTGGAGTCGACGAACAATGA
66 AAGAAGCGGGATGAAGCTCTGGAGTCGACGAACAATGA
1380207 T
1 T
1380208 TTTGGTGATG
Statistics
Matches: 96, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
103 96 1.00
ACGTcount: A:0.32, C:0.13, G:0.29, T:0.26
Consensus pattern (103 bp):
TGGTTGATAACAATATTTTCAGTGATAAAGCGGCCCAAAATGAAGCTTGTTTGGTTCAGAGAAAC
AAGAAGCGGGATGAAGCTCTGGAGTCGACGAACAATGA
Found at i:1387923 original size:23 final size:23
Alignment explanation
Indices: 1387893--1387941 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
1387883 TGGTGGTTGG
*
1387893 TTTAATGG-ATGTTTAGACTTTAT
1 TTTAATGGTATATTTA-ACTTTAT
*
1387916 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
1387939 TTT
1 TTT
1387942 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:1394492 original size:7 final size:7
Alignment explanation
Indices: 1394480--1394504 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1394470 TGTGCATAAA
1394480 TAAAATT
1 TAAAATT
1394487 TAAAATT
1 TAAAATT
1394494 TAAAATT
1 TAAAATT
1394501 TAAA
1 TAAA
1394505 CTTTTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
TAAAATT
Found at i:1394516 original size:5 final size:5
Alignment explanation
Indices: 1394506--1394534 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1394496 AAATTTAAAC
1394506 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1394535 GCAATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:1398160 original size:23 final size:23
Alignment explanation
Indices: 1398130--1398178 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
1398120 TGGTGGTTGG
*
1398130 TTTAATGG-ATGTTTAGACTTTAT
1 TTTAATGGTATATTTA-ACTTTAT
*
1398153 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
1398176 TTT
1 TTT
1398179 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:1398694 original size:11 final size:10
Alignment explanation
Indices: 1398670--1398699 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
1398660 TTCTTTTCAT
1398670 TTTATTTATG
1 TTTATTTATG
1398680 TTTATTTACTG
1 TTTATTTA-TG
1398691 TTTATTTAT
1 TTTATTTAT
1398700 CATTTTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.20, C:0.03, G:0.07, T:0.70
Consensus pattern (10 bp):
TTTATTTATG
Found at i:1401475 original size:38 final size:39
Alignment explanation
Indices: 1401433--1401530 Score: 112
Period size: 38 Copynumber: 2.6 Consensus size: 39
1401423 TTTTAAAACT
1401433 AATATTATATATA-TTTCGAAAAACATTTTC-AAAACCCA
1 AATATTATATATAGTTTCGAAAAACATTTTCTAAAA-CCA
* ** *
1401471 AATATTATATATAGTTTCG-AACATGTTTTCTAAAACTA
1 AATATTATATATAGTTTCGAAAAACATTTTCTAAAACCA
* *
1401509 TATATTATATATATTTTCGAAA
1 AATATTATATATAGTTTCGAAA
1401531 CTATATTATA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
38 40 0.78
39 11 0.22
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (39 bp):
AATATTATATATAGTTTCGAAAAACATTTTCTAAAACCA
Found at i:1401619 original size:68 final size:69
Alignment explanation
Indices: 1401470--1401604 Score: 159
Period size: 68 Copynumber: 1.9 Consensus size: 69
1401460 TTCAAAACCC
* * *
1401470 AAATATTATATATAGTTTCGAACATGTTTTCTAAAACTATATATTATATATATTTTCGAAACTAT
1 AAATA-TATATATA--TTCAAAAATGTTTTCTAAAACTATATATTATATATATTTTCGAAACAAT
1401535 ATTATAT
63 ATTATAT
* * *
1401542 ATAGATATATATATTCAAAAATGTTTT-TAAAACTATATATTATATATTTTGTTC-AAA-AATAT
1 AAATATATATATATTCAAAAATGTTTTCTAAAACTATATATTATATATATT-TTCGAAACAATAT
1401604 T
65 T
1401605 TTCAAAACTA
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
67 5 0.09
68 25 0.45
69 15 0.27
71 8 0.14
72 3 0.05
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (69 bp):
AAATATATATATATTCAAAAATGTTTTCTAAAACTATATATTATATATATTTTCGAAACAATATT
ATAT
Found at i:1401648 original size:48 final size:46
Alignment explanation
Indices: 1401575--1401794 Score: 163
Period size: 39 Copynumber: 5.3 Consensus size: 46
1401565 TTTTTAAAAC
1401575 TATATAT-TATATATTTTGTTCAAAAATA-TTTTCAAAACTATATAT
1 TATATATATATATATTTTGTTCAAAAA-ACTTTTCAAAACTATATAT
*
1401620 TATATATATATATATTTTTTTTCAAAAAAACTTTTCAAAAC----TA-
1 TATATATATATATA-TTTTGTTC-AAAAAACTTTTCAAAACTATATAT
*
1401663 TGTAT-TATATATA--TT-TTC-AAAAACGTTTTCAAAACTATA---
1 TATATATATATATATTTTGTTCAAAAAAC-TTTTCAAAACTATATAT
1401702 --TAT-TATATATATTTT-TTC-AAAAACTTTTTCAAAACTATATA-
1 TATATATATATATATTTTGTTCAAAAAAC-TTTTCAAAACTATATAT
**
1401743 T-TATATATATATA-----TTCAAAAATGTTTTCAAAACTATATAT
1 TATATATATATATATTTTGTTCAAAAAACTTTTCAAAACTATATAT
1401783 TATATATA-ATAT
1 TATATATATATAT
1401795 GTATATATTA
Statistics
Matches: 152, Mismatches: 5, Indels: 41
0.77 0.03 0.21
Matches are distributed among these distances:
36 6 0.04
37 21 0.14
38 3 0.02
39 46 0.30
40 9 0.06
41 6 0.04
42 11 0.07
43 12 0.08
44 2 0.01
45 7 0.05
46 6 0.04
47 8 0.05
48 15 0.10
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (46 bp):
TATATATATATATATTTTGTTCAAAAAACTTTTCAAAACTATATAT
Found at i:1401719 original size:39 final size:39
Alignment explanation
Indices: 1401620--1401790 Score: 240
Period size: 39 Copynumber: 4.4 Consensus size: 39
1401610 AACTATATAT
*
1401620 TATATATATATATATTTTTTTTCAAAAAAAC-TTTTCAAAAC
1 TATATAT-TATATATATTTTTTC--AAAAACGTTTTCAAAAC
*
1401661 TATGTATTATATATA--TTTTCAAAAACGTTTTCAAAAC
1 TATATATTATATATATTTTTTCAAAAACGTTTTCAAAAC
*
1401698 TATATATTATATATATTTTTTCAAAAACTTTTTCAAAAC
1 TATATATTATATATATTTTTTCAAAAACGTTTTCAAAAC
* * *
1401737 TATATATTATATATATATATTCAAAAATGTTTTCAAAAC
1 TATATATTATATATATTTTTTCAAAAACGTTTTCAAAAC
1401776 TATATATTATATATA
1 TATATATTATATATA
1401791 ATATGTATAT
Statistics
Matches: 119, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
36 6 0.05
37 24 0.20
38 5 0.04
39 71 0.60
40 7 0.06
41 6 0.05
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.46
Consensus pattern (39 bp):
TATATATTATATATATTTTTTCAAAAACGTTTTCAAAAC
Found at i:1407087 original size:21 final size:21
Alignment explanation
Indices: 1407021--1407087 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 21
1407011 CATAAAATGA
1407021 AAGAAAATTAAATTCTAAAAGAG
1 AAGAAAATTAAATTC-AAAAG-G
* * *
1407044 ATG-AAA-TGAATTACATAATGG
1 AAGAAAATTAAATT-CA-AAAGG
1407065 AAGAAAATTAAATTCAAAAGG
1 AAGAAAATTAAATTCAAAAGG
1407086 AA
1 AA
1407088 ATGAAATAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
21 15 0.44
22 12 0.35
23 7 0.21
ACGTcount: A:0.58, C:0.04, G:0.15, T:0.22
Consensus pattern (21 bp):
AAGAAAATTAAATTCAAAAGG
Found at i:1413934 original size:22 final size:22
Alignment explanation
Indices: 1413900--1413941 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1413890 AAAAAAGAAA
*
1413900 TAAAAAAGTTTAAATAAAAAAT
1 TAAAAAAGATTAAATAAAAAAT
* *
1413922 TAAAAAGGATTAAATTAAAA
1 TAAAAAAGATTAAATAAAAA
1413942 TAAATTGAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (22 bp):
TAAAAAAGATTAAATAAAAAAT
Found at i:1415075 original size:14 final size:14
Alignment explanation
Indices: 1415038--1415087 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
1415028 TATTGGACCT
1415038 AAAAAATAAAAATA
1 AAAAAATAAAAATA
1415052 AAAAACATAAAAATA
1 AAAAA-ATAAAAATA
** *
1415067 AAGGAATAATAATA
1 AAAAAATAAAAATA
1415081 AACAAAA
1 AA-AAAA
1415088 AATAAGTATA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
14 15 0.52
15 14 0.48
ACGTcount: A:0.78, C:0.04, G:0.04, T:0.14
Consensus pattern (14 bp):
AAAAAATAAAAATA
Found at i:1415285 original size:38 final size:37
Alignment explanation
Indices: 1415102--1415285 Score: 192
Period size: 38 Copynumber: 4.9 Consensus size: 37
1415092 AGTATACTAT
* *
1415102 AAAACATTTT-AAAACTA-ATATTATATATATTTTGA
1 AAAACGTTTTCAAAACTATATATTATATATATTTTCA
* * * * * *
1415137 AAAACATTTTCAAACCCCAAATATTATATATAGTTTCC
1 AAAACGTTTTCAAA-ACTATATATTATATATATTTTCA
* *
1415175 AACATGTTTTCTAAAACTATATATTATATATATTTTCGA
1 AAAACGTTTTC-AAAACTATATATTATATATATTTTC-A
*
1415214 AAAATGTTTTCAAAACTATATATTATATATATATTTTTCA
1 AAAACGTTTTCAAAACTATATA-T-TATATATA-TTTTCA
*
1415254 AAAACGTTTTCAAAACTATATATTATCTATAT
1 AAAACGTTTTCAAAACTATATATTATATATAT
1415286 ATTAAATAGA
Statistics
Matches: 125, Mismatches: 16, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
35 10 0.08
36 3 0.02
37 3 0.02
38 59 0.47
39 15 0.12
40 30 0.24
41 5 0.04
ACGTcount: A:0.43, C:0.11, G:0.03, T:0.42
Consensus pattern (37 bp):
AAAACGTTTTCAAAACTATATATTATATATATTTTCA
Found at i:1421016 original size:19 final size:19
Alignment explanation
Indices: 1420992--1421089 Score: 69
Period size: 19 Copynumber: 5.2 Consensus size: 19
1420982 TACCATTAAG
1420992 TTTAAACGATTATATATGA
1 TTTAAACGATTATATATGA
** ** *
1421011 TTTAAAATAACATGATAT-T
1 TTTAAACGATTAT-ATATGA
1421030 TTTAAACGATTATATATGA
1 TTTAAACGATTATATATGA
* *
1421049 TTT-AAC-ATAACATGATAT-T
1 TTTAAACGAT--TAT-ATATGA
1421068 TTTAAACGATTATATATGA
1 TTTAAACGATTATATATGA
1421087 TTT
1 TTT
1421090 TAATTAATAT
Statistics
Matches: 57, Mismatches: 14, Indels: 16
0.66 0.16 0.18
Matches are distributed among these distances:
17 2 0.04
18 11 0.19
19 31 0.54
20 11 0.19
21 2 0.04
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (19 bp):
TTTAAACGATTATATATGA
Found at i:1421043 original size:38 final size:38
Alignment explanation
Indices: 1420992--1421089 Score: 187
Period size: 38 Copynumber: 2.6 Consensus size: 38
1420982 TACCATTAAG
1420992 TTTAAACGATTATATATGATTTAAAATAACATGATATT
1 TTTAAACGATTATATATGATTTAAAATAACATGATATT
*
1421030 TTTAAACGATTATATATGATTTAACATAACATGATATT
1 TTTAAACGATTATATATGATTTAAAATAACATGATATT
1421068 TTTAAACGATTATATATGATTT
1 TTTAAACGATTATATATGATTT
1421090 TAATTAATAT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 59 1.00
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (38 bp):
TTTAAACGATTATATATGATTTAAAATAACATGATATT
Found at i:1421633 original size:10 final size:11
Alignment explanation
Indices: 1421620--1421682 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 11
1421610 ACACGGTAGG
1421620 CATCCGAG-GC
1 CATCCGAGAGC
1421630 CATCCGAGAAGC
1 CATCCGAG-AGC
* *
1421642 TATGCGAGAG-
1 CATCCGAGAGC
1421652 CATCCGAG-GC
1 CATCCGAGAGC
1421662 CATCCGACCGAGGC
1 CATCCGA--GA-GC
1421676 CATCCGA
1 CATCCGA
1421683 CCGAATTATG
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
9 1 0.02
10 21 0.50
11 2 0.05
12 9 0.21
14 9 0.21
ACGTcount: A:0.25, C:0.35, G:0.29, T:0.11
Consensus pattern (11 bp):
CATCCGAGAGC
Found at i:1421674 original size:14 final size:14
Alignment explanation
Indices: 1421655--1421686 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
1421645 GCGAGAGCAT
1421655 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
1421669 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
1421683 CCGA
1 CCGA
1421687 ATTATGTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.22, C:0.44, G:0.28, T:0.06
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:1421797 original size:29 final size:29
Alignment explanation
Indices: 1421755--1421868 Score: 165
Period size: 29 Copynumber: 3.9 Consensus size: 29
1421745 GAGCAAGGGT
* *
1421755 AGGTCGCCCGGAGTGCATGGCGATCTACA
1 AGGTCGCCAGGAGTGCATGGCGACCTACA
1421784 AGGTCGCCAGGAGTGCATGGCGACCTACA
1 AGGTCGCCAGGAGTGCATGGCGACCTACA
* *
1421813 AGGTCGCCAGGATTGTATGGCGACCTACA
1 AGGTCGCCAGGAGTGCATGGCGACCTACA
* * *
1421842 AGGTCGCCCGGAGGGCATGGCAACCTA
1 AGGTCGCCAGGAGTGCATGGCGACCTA
1421869 TGCTTGGGAA
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 76 1.00
ACGTcount: A:0.23, C:0.27, G:0.34, T:0.16
Consensus pattern (29 bp):
AGGTCGCCAGGAGTGCATGGCGACCTACA
Found at i:1423062 original size:27 final size:27
Alignment explanation
Indices: 1423032--1423085 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
1423022 GGCCATAGCT
*
1423032 GCCGCAAGAATAACATATCGTTTGGAG
1 GCCGCAAGAATAACATATCGTTGGGAG
*
1423059 GCCGCAAGAATAGCATATCGTTGGGAG
1 GCCGCAAGAATAACATATCGTTGGGAG
1423086 TGACTCATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.31, C:0.19, G:0.30, T:0.20
Consensus pattern (27 bp):
GCCGCAAGAATAACATATCGTTGGGAG
Found at i:1424317 original size:15 final size:15
Alignment explanation
Indices: 1424299--1424328 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1424289 AAAACCATGT
1424299 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
1424314 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
1424329 GAAATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (15 bp):
TAGATAAAAAGGTAA
Found at i:1424335 original size:15 final size:15
Alignment explanation
Indices: 1424302--1424336 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1424292 ACCATGTTAG
* *
1424302 ATAAAAAGGTAATAG
1 ATAAAAAGGTAAGAA
1424317 ATAAAAAGGTAAGAA
1 ATAAAAAGGTAAGAA
1424332 ATAAA
1 ATAAA
1424337 TAAATAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (15 bp):
ATAAAAAGGTAAGAA
Found at i:1424359 original size:5 final size:5
Alignment explanation
Indices: 1424330--1424522 Score: 57
Period size: 5 Copynumber: 38.6 Consensus size: 5
1424320 AAAAGGTAAG
* * * * *
1424330 AAAT- AAAT- AAATA AATTA AATTA AAATA AAGAGA AAA-C AAATT AAATAA
1 AAATA AAATA AAATA AAATA AAATA AAATA AA-ATA AAATA AAATA AAAT-A
* * * * *
1424379 AAGATA AGAT- AAAGA AAACA AAGATA AAATA GTAAGTA AAATA ATATA
1 AA-ATA AAATA AAATA AAATA AA-ATA AAATA --AAATA AAATA AAATA
* * * * *
1424427 AAAAA TAAAGA AAA-A GAAGA AAA-A ATATA GAAATA AAA-A AAAT- AAATA
1 AAATA -AAATA AAATA AAATA AAATA AAATA -AAATA AAATA AAATA AAATA
* *
1424475 AAATA ATAATAA AAAGTA AAATA ATAT- ATATA AAAT- AAA-A AAATA
1 AAATA A-AAT-A AAA-TA AAATA AAATA AAATA AAATA AAATA AAATA
1424520 AAA
1 AAA
1424523 AAGTAAATAT
Statistics
Matches: 145, Mismatches: 23, Indels: 41
0.69 0.11 0.20
Matches are distributed among these distances:
4 37 0.26
5 70 0.48
6 29 0.20
7 9 0.06
ACGTcount: A:0.73, C:0.01, G:0.07, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:1424466 original size:15 final size:16
Alignment explanation
Indices: 1424446--1424544 Score: 55
Period size: 19 Copynumber: 6.0 Consensus size: 16
1424436 GAAAAAGAAG
*
1424446 AAAA-AATATAGAAAT
1 AAAATAATATAAAAAT
*
1424461 AAAA-AA-A-ATAAAT
1 AAAATAATATAAAAAT
1424474 AAAATAATAATAAAAAGT
1 AAAATAAT-ATAAAAA-T
1424492 AAAATAATATATATAAAAT
1 AAAAT-A-ATATA-AAAAT
*
1424511 AAAAAAATA-AAAAAGT
1 AAAATAATATAAAAA-T
*
1424527 AAATATATATATATAAAT
1 AAA-ATA-ATATAAAAAT
1424545 TAATAAAACT
Statistics
Matches: 67, Mismatches: 5, Indels: 21
0.72 0.05 0.23
Matches are distributed among these distances:
13 9 0.13
14 3 0.04
15 10 0.15
16 6 0.09
17 9 0.13
18 11 0.16
19 13 0.19
20 6 0.09
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (16 bp):
AAAATAATATAAAAAT
Found at i:1424477 original size:27 final size:26
Alignment explanation
Indices: 1424428--1424521 Score: 72
Period size: 26 Copynumber: 3.7 Consensus size: 26
1424418 AATAATATAA
*
1424428 AAAATAAAGAAAAAGAAGA-AAAAATAT
1 AAAATAAA-AAAAATAA-ATAAAAATAT
1424455 AGAAATAAAAAAAATAAAT-AAAATA-
1 A-AAATAAAAAAAATAAATAAAAATAT
* ** *
1424480 ATAATAAAAAGTA-AAATAATATATAT
1 AAAATAAAAAAAATAAATAA-AAATAT
1424506 AAAAT-AAAAAAATAAA
1 AAAATAAAAAAAATAAA
1424522 AAAGTAAATA
Statistics
Matches: 53, Mismatches: 8, Indels: 13
0.72 0.11 0.18
Matches are distributed among these distances:
23 4 0.08
24 10 0.19
25 10 0.19
26 14 0.26
27 8 0.15
28 7 0.13
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (26 bp):
AAAATAAAAAAAATAAATAAAAATAT
Found at i:1424504 original size:49 final size:48
Alignment explanation
Indices: 1424416--1424521 Score: 119
Period size: 49 Copynumber: 2.2 Consensus size: 48
1424406 AATAGTAAGT
1424416 AAAATAATATAAAAAATAAAGAAAAAGAAGAAAAAATATAG-AAATAAAA
1 AAAATAA-ATAAAAAATAAAGAAAAAGAAGAAAAAATATAGAAAAT-AAA
* * *
1424465 AAAATAAATAAAATAAT-AATAAAAAGTAA-AATAATATATATAAAATAAA
1 AAAATAAATAAAA-AATAAAGAAAAAG-AAGAA-AAAATATAGAAAATAAA
1424514 AAAATAAA
1 AAAATAAA
1424522 AAAGTAAATA
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
48 16 0.32
49 30 0.60
50 4 0.08
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (48 bp):
AAAATAAATAAAAAATAAAGAAAAAGAAGAAAAAATATAGAAAATAAA
Found at i:1424523 original size:9 final size:9
Alignment explanation
Indices: 1424416--1424524 Score: 60
Period size: 9 Copynumber: 11.6 Consensus size: 9
1424406 AATAGTAAGT
*
1424416 AAAATAATA
1 AAAAAAATA
*
1424425 TAAAAAATA
1 AAAAAAATA
*
1424434 AAGAAAAAGA
1 AA-AAAAATA
1424444 AGAAAAAAT-
1 A-AAAAAATA
* *
1424453 ATAGAAATA
1 AAAAAAATA
1424462 AAAAAAATAA
1 AAAAAAAT-A
1424472 ATAAAATAATA
1 A-AAAA-AATA
*
1424483 ATAAAAAGTA
1 A-AAAAAATA
*
1424493 AAATAATATA
1 AAA-AAAATA
* *
1424503 TATAAAAT-
1 AAAAAAATA
1424511 AAAAAAATA
1 AAAAAAATA
1424520 AAAAA
1 AAAAA
1424525 GTAAATATAT
Statistics
Matches: 75, Mismatches: 17, Indels: 16
0.69 0.16 0.15
Matches are distributed among these distances:
8 11 0.15
9 26 0.35
10 23 0.31
11 12 0.16
12 3 0.04
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (9 bp):
AAAAAAATA
Found at i:1424532 original size:27 final size:26
Alignment explanation
Indices: 1424416--1424533 Score: 86
Period size: 27 Copynumber: 4.5 Consensus size: 26
1424406 AATAGTAAGT
*
1424416 AAAATAATATAAAAAATAAAGAAAA-AGA
1 AAAATAA-ATATAAAATAAA-AAAATA-A
1424444 AGAAA-AAATATAGAAAT-AAAAAA-AA
1 A-AAATAAATATA-AAATAAAAAAATAA
* *
1424469 TAAATAAA-ATAATAAT-AAAAAGTAA
1 AAAATAAATATAA-AATAAAAAAATAA
*
1424494 AATAATATATATAAAATAAAAAAATAA
1 AA-AATAAATATAAAATAAAAAAATAA
1424521 AAAAGTAAATATA
1 AAAA-TAAATATA
1424534 TATATATAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 19
0.74 0.07 0.19
Matches are distributed among these distances:
23 1 0.01
24 14 0.19
25 7 0.09
26 15 0.20
27 27 0.36
28 7 0.09
29 3 0.04
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.19
Consensus pattern (26 bp):
AAAATAAATATAAAATAAAAAAATAA
Found at i:1424537 original size:35 final size:37
Alignment explanation
Indices: 1424470--1424603 Score: 114
Period size: 35 Copynumber: 3.5 Consensus size: 37
1424460 TAAAAAAAAT
*
1424470 AAATAAAATAATAATAAAAAGTAAAATAATATATATA
1 AAATAAAAAAATAATAAAAAGTAAAATAATATATATA
1424507 AAATAAAAAAAT-A-AAAAAGT-AAATATATATATATA
1 AAATAAAAAAATAATAAAAAGTAAAATA-ATATATATA
* * * *
1424542 AATTAATAAAACTGATAATAAAAAATAATATATTTATATATA
1 AAATAA-AAAA---ATAATAAAAAGTAAAATA-ATATATATA
* *
1424584 TAATCTAAAAAA-AATAAAAA
1 AAAT-AAAAAAATAATAAAAA
1424604 TATATACTAA
Statistics
Matches: 80, Mismatches: 8, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
34 5 0.06
35 21 0.26
36 5 0.06
37 11 0.14
38 8 0.10
39 3 0.04
40 1 0.01
41 6 0.08
42 19 0.24
43 1 0.01
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.28
Consensus pattern (37 bp):
AAATAAAAAAATAATAAAAAGTAAAATAATATATATA
Found at i:1424565 original size:42 final size:39
Alignment explanation
Indices: 1424466--1424587 Score: 116
Period size: 37 Copynumber: 3.2 Consensus size: 39
1424456 GAAATAAAAA
1424466 AAATAAATAAAATAATAAT-AAAAAGTAAA-ATA-ATATAT
1 AAAT-AATAAAAT-ATAATAAAAAAGTAAATATATATATAT
1424504 ATAA-AATAAAA-A-AATAAAAAAGTAAATATATATATAT
1 A-AATAATAAAATATAATAAAAAAGTAAATATATATATAT
*
1424541 AAATTAATAAAACTGATAATAAAAAA-T-AATATATTTATAT
1 AAA-TAATAAAA-T-ATAATAAAAAAGTAAATATATATATAT
*
1424581 ATATAAT
1 AAATAAT
1424588 CTAAAAAAAA
Statistics
Matches: 72, Mismatches: 2, Indels: 19
0.77 0.02 0.20
Matches are distributed among these distances:
34 3 0.04
35 11 0.15
36 5 0.07
37 14 0.19
38 8 0.11
39 6 0.08
40 14 0.19
41 2 0.03
42 9 0.12
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.30
Consensus pattern (39 bp):
AAATAATAAAATATAATAAAAAAGTAAATATATATATAT
Found at i:1424655 original size:24 final size:23
Alignment explanation
Indices: 1424594--1424661 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 23
1424584 TAATCTAAAA
1424594 AAAATAAAAATATATAC-T-AAAGT
1 AAAA-AAAAATAT-TACATAAAAGT
1424617 AAAAAAGAAA-A-TACATAAAATGT
1 AAAAAA-AAATATTACATAAAA-GT
1424640 AAAAAAAAATATTACATGAAAA
1 AAAAAAAAATATTACAT-AAAA
1424662 AAAAAGAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
20 3 0.08
21 1 0.03
22 9 0.24
23 16 0.42
24 5 0.13
25 4 0.11
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.21
Consensus pattern (23 bp):
AAAAAAAAATATTACATAAAAGT
Found at i:1425029 original size:34 final size:34
Alignment explanation
Indices: 1424986--1425054 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
1424976 GAATCCTAGC
1424986 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
* *
1425020 AAAATTCTATCCTATTTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
1425054 A
1 A
1425055 GTAGGACGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (34 bp):
AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
Found at i:1425819 original size:98 final size:98
Alignment explanation
Indices: 1425650--1425841 Score: 276
Period size: 98 Copynumber: 2.0 Consensus size: 98
1425640 TGGAACCGGA
* * *
1425650 AAATTGTTTGTTGACAACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCA
1 AAATTGTTTGTTGACAACCAGCCACCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCA
* * *
1425715 ATATCCTTCGTTGTGAAGTTGAGATTGGCTCCG
66 ATATCCTCCGCTGTGAAGTTGAAATTGGCTCCG
** * * * *
1425748 AAATTGTTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCCA
1 AAATTGTTTGTTGACAACCAGCCACCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCA
1425813 ATATCCTCCGCTGTGAAGTTGAAATTGGC
66 ATATCCTCCGCTGTGAAGTTGAAATTGGC
1425842 CCTGAAACTG
Statistics
Matches: 82, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
98 82 1.00
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.34
Consensus pattern (98 bp):
AAATTGTTTGTTGACAACCAGCCACCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCA
ATATCCTCCGCTGTGAAGTTGAAATTGGCTCCG
Found at i:1426651 original size:67 final size:66
Alignment explanation
Indices: 1426518--1426685 Score: 221
Period size: 68 Copynumber: 2.5 Consensus size: 66
1426508 AAGATATCTG
* * * **
1426518 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTATGTTTTAAGGGAAATAAATTCAAAGA-
1426583 TT
65 TT
* * *
1426585 TGTGTTTCAAGAGTAATTGTCTCAAGGGAGACAAAATT-TGTTTTAGGGGAAATAAATTCAAAGA
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTATGTTTTAAGGGAAATAAATTCAAAGA
1426649 TT
65 TT
* *
1426651 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
1426686 CTTAGTTCCA
Statistics
Matches: 88, Mismatches: 12, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
65 30 0.34
66 3 0.03
67 24 0.27
68 31 0.35
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.31
Consensus pattern (66 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTATGTTTTAAGGGAAATAAATTCAAAGAT
T
Found at i:1426755 original size:101 final size:101
Alignment explanation
Indices: 1426602--1426896 Score: 326
Period size: 101 Copynumber: 2.9 Consensus size: 101
1426592 CAAGAGTAAT
* * ** * * * *
1426602 TGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAGGGAAAC
1 TGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAAAATTTTGTTTCAAGGGAAAC
1426667 TGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAC
66 TGTCTCAAGAGAGACAAAACTTA-TTCCAAAAGAAAC
*
1426704 TGTCTCAAGGGAGACGAAA-TTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGAAAC
1 TGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAAAATTTTGTTTCAAGGGAAAC
* * **
1426768 TGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAAC
66 TGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAAC
** * *
1426804 TGTCTCAAGATAGACGAAATTTGTTTC-AAGAGAAAC-TGTCTCAAGAGAGACAAAATTTGTTTC
1 TGTCTCAAGGGAGACGAAATTTGTTTCAAAGA-AAACATAT-TC-----A-A-AAATTTTGTTTC
1426867 AAGGGAAACTGTCTCAAGAGAGACAAAACT
57 AAGGGAAACTGTCTCAAGAGAGACAAAACT
1426897 CTTCTAGTGA
Statistics
Matches: 165, Mismatches: 18, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
100 33 0.20
101 73 0.44
102 18 0.11
106 1 0.01
107 1 0.01
108 39 0.24
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (101 bp):
TGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAAAATTTTGTTTCAAGGGAAAC
TGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAAC
Found at i:1426802 original size:36 final size:36
Alignment explanation
Indices: 1426751--1426894 Score: 252
Period size: 36 Copynumber: 4.0 Consensus size: 36
1426741 ATTCAAATAT
1426751 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * *
1426787 TTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
1426823 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1426859 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1426895 CTCTTCTAGT
Statistics
Matches: 100, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 100 1.00
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.26
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:1427401 original size:18 final size:18
Alignment explanation
Indices: 1427374--1427409 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1427364 TGTTGAATCC
* *
1427374 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
1427392 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
1427410 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:1427852 original size:22 final size:22
Alignment explanation
Indices: 1427826--1427880 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
1427816 TTGTGTTTGG
1427826 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
1427848 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
1427870 TCAAAGGTTTG
1 TCAAAGGTTTG
1427881 ATGGGATAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:1428535 original size:22 final size:22
Alignment explanation
Indices: 1428501--1428581 Score: 69
Period size: 22 Copynumber: 3.7 Consensus size: 22
1428491 TTGCATGTGC
* *
1428501 TTTTTTTCCCTTTTTCTTTTTG
1 TTTTTTGCTCTTTTTCTTTTTG
*
1428523 ATTTTTGCTC-TTTT-TTTTTG
1 TTTTTTGCTCTTTTTCTTTTTG
* *
1428543 TTCTTGTTTCTCTTTTTCTTTGTTT
1 TT-TT-TTGCTCTTTTTCTTT-TTG
1428568 TTTTTTGCT-TTTTT
1 TTTTTTGCTCTTTTT
1428582 GCTTCTTTTC
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
20 7 0.15
21 6 0.13
22 17 0.36
23 8 0.17
24 5 0.11
25 4 0.09
ACGTcount: A:0.01, C:0.14, G:0.07, T:0.78
Consensus pattern (22 bp):
TTTTTTGCTCTTTTTCTTTTTG
Found at i:1428596 original size:16 final size:16
Alignment explanation
Indices: 1428553--1428603 Score: 54
Period size: 15 Copynumber: 3.2 Consensus size: 16
1428543 TTCTTGTTTC
*
1428553 TCTTTTTCTTTGTTT-T
1 TCTTTTGCTTT-TTTGT
1428569 T-TTTTGCTTTTTTGCT
1 TCTTTTGCTTTTTTG-T
1428585 TCTTTT-CTTTTTTGT
1 TCTTTTGCTTTTTTGT
1428600 TCTT
1 TCTT
1428604 GATTGGATCT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 3 0.10
15 13 0.42
16 11 0.35
17 4 0.13
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.78
Consensus pattern (16 bp):
TCTTTTGCTTTTTTGT
Found at i:1431592 original size:15 final size:15
Alignment explanation
Indices: 1431574--1431603 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1431564 AAAACCATGT
1431574 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
1431589 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
1431604 GAAATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (15 bp):
TAGATAAAAAGGTAA
Found at i:1431610 original size:15 final size:15
Alignment explanation
Indices: 1431577--1431611 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1431567 ACCATGTTAG
* *
1431577 ATAAAAAGGTAATAG
1 ATAAAAAGGTAAGAA
1431592 ATAAAAAGGTAAGAA
1 ATAAAAAGGTAAGAA
1431607 ATAAA
1 ATAAA
1431612 TAAATTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (15 bp):
ATAAAAAGGTAAGAA
Found at i:1431723 original size:8 final size:9
Alignment explanation
Indices: 1431708--1431733 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1431698 TATAAAAATA
1431708 AAGAAAAAG
1 AAGAAAAAG
1431717 AAGAAAAAG
1 AAGAAAAAG
1431726 AAGAAAAA
1 AAGAAAAA
1431734 ATATAGAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
AAGAAAAAG
Found at i:1431782 original size:38 final size:39
Alignment explanation
Indices: 1431740--1431842 Score: 97
Period size: 41 Copynumber: 2.6 Consensus size: 39
1431730 AAAAATATAG
*
1431740 AAATAA-A-ACAAATA-AATAAAATAATAATAAAAAAGTAA
1 AAATAATATACAAATATAATAAAAAAAT-A-AAAAAAGTAA
* *
1431778 AAATAATATATATATATAATAAAAAAATAAAAAAAGTAA
1 AAATAATATACAAATATAATAAAAAAATAAAAAAAGTAA
*
1431817 ATATATATATATATAAAT-TAATAAAA
1 A-A-ATA-ATATACAAATATAATAAAA
1431843 CTGATAATAA
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
38 6 0.11
39 12 0.22
40 7 0.13
41 21 0.38
42 9 0.16
ACGTcount: A:0.71, C:0.01, G:0.02, T:0.26
Consensus pattern (39 bp):
AAATAATATACAAATATAATAAAAAAATAAAAAAAGTAA
Found at i:1431798 original size:30 final size:30
Alignment explanation
Indices: 1431740--1431825 Score: 95
Period size: 30 Copynumber: 2.8 Consensus size: 30
1431730 AAAAATATAG
*
1431740 AAATAAAACAAA-TAAATAAAATAATAATAAAA
1 AAATAAAA-AAAGTAAAT-ATAT-ATAATAAAA
* *
1431772 AAGTAAAAATAA-TATATATATATAATAAAA
1 AAATAAAAA-AAGTAAATATATATAATAAAA
1431802 AAATAAAAAAAGTAAATATATATA
1 AAATAAAAAAAGTAAATATATATA
1431826 TATATAAATT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
29 2 0.04
30 28 0.60
31 4 0.09
32 13 0.28
ACGTcount: A:0.72, C:0.01, G:0.02, T:0.24
Consensus pattern (30 bp):
AAATAAAAAAAGTAAATATATATAATAAAA
Found at i:1431863 original size:38 final size:35
Alignment explanation
Indices: 1431776--1431892 Score: 101
Period size: 44 Copynumber: 3.0 Consensus size: 35
1431766 ATAAAAAAGT
1431776 AAAAATAATATATATATATAATAAAAAAATAAAAA
1 AAAAATAATATATATATATAATAAAAAAATAAAAA
1431811 AAGTAAAT-ATATATATATATAAATTAATAAAACTGATAATAAA
1 AA--AAATAATATATATATAT-AA-TAA-AAAA---ATAA-AAA
*
1431854 AAATAATATATTTATATATATAATCTAAAAAAATAAAAA
1 AAA-AATA-ATATATATATATAA--TAAAAAAATAAAAA
1431893 TATATACTAA
Statistics
Matches: 67, Mismatches: 2, Indels: 22
0.74 0.02 0.24
Matches are distributed among these distances:
35 2 0.03
36 12 0.18
37 6 0.09
38 3 0.04
39 7 0.10
40 4 0.06
41 1 0.01
42 7 0.10
43 11 0.16
44 14 0.21
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (35 bp):
AAAAATAATATATATATATAATAAAAAAATAAAAA
Found at i:1431909 original size:23 final size:21
Alignment explanation
Indices: 1431883--1431957 Score: 59
Period size: 24 Copynumber: 3.5 Consensus size: 21
1431873 ATAATCTAAA
1431883 AAAATAAAAATATATACTAAA-GT
1 AAAA-AAAAATATATA--AAATGT
*
1431906 AAAAAAGAAAATACATAAAATGT
1 -AAAAA-AAAATATATAAAATGT
*
1431929 AAAAAAAAATAT-T-ACATG-
1 AAAAAAAAATATATAAAATGT
1431947 AAAAAAAAATA
1 AAAAAAAAATA
1431958 ACAAAACAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
18 11 0.24
19 4 0.09
20 1 0.02
21 6 0.13
22 8 0.17
23 3 0.07
24 13 0.28
ACGTcount: A:0.71, C:0.04, G:0.05, T:0.20
Consensus pattern (21 bp):
AAAAAAAAATATATAAAATGT
Found at i:1431944 original size:24 final size:23
Alignment explanation
Indices: 1431883--1431950 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 23
1431873 ATAATCTAAA
1431883 AAAATAAAAATATATAC-T-AAAGT
1 AAAA-AAAAATAT-TACATAAAAGT
1431906 AAAAAAGAAA-A-TACATAAAATGT
1 AAAAAA-AAATATTACATAAAA-GT
1431929 AAAAAAAAATATTACATGAAAA
1 AAAAAAAAATATTACAT-AAAA
1431951 AAAAATAACA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
20 3 0.08
21 1 0.03
22 9 0.24
23 16 0.42
24 5 0.13
25 4 0.11
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.21
Consensus pattern (23 bp):
AAAAAAAAATATTACATAAAAGT
Found at i:1432308 original size:34 final size:34
Alignment explanation
Indices: 1432265--1432333 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
1432255 GAATCCTAGC
1432265 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
*
1432299 AAAATTCTATCATATTTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
1432333 A
1 A
1432334 GTAGGACGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (34 bp):
AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
Found at i:1432761 original size:47 final size:48
Alignment explanation
Indices: 1432663--1432937 Score: 358
Period size: 48 Copynumber: 5.6 Consensus size: 48
1432653 TATTAGTATT
*
1432663 AATATAAGAATATATTAGTATAGTTTTCAAATGTAGTATATGGTTTTA
1 AATATTAGAATATATTAGTATAGTTTTCAAATGTAGTATATGGTTTTA
* *
1432711 AATATTCGAATATATTAGTATAGTTTTC-AATGTAGTATATGGTTTAA
1 AATATTAGAATATATTAGTATAGTTTTCAAATGTAGTATATGGTTTTA
1432758 AATATTAGAATATATTAGTATAGTTTTCAAATGTAGTATATGGTTTTA
1 AATATTAGAATATATTAGTATAGTTTTCAAATGTAGTATATGGTTTTA
*
1432806 AATATTAGAATATATTAGTATAGTTTTC-AATGTAGTGTATGGTTTT-
1 AATATTAGAATATATTAGTATAGTTTTCAAATGTAGTATATGGTTTTA
* * * * * *
1432852 AATTTTCAGATTATGTATTAGTATATGTAGTGCGTAATTTTTAGTATATGGTTTTA
1 AATATT-AGA--ATATATTAGTATA-GT-TTTC--AA-ATGTAGTATATGGTTTTA
*
1432908 AATATTAGAATATAGTAGTATAGTTTTCAA
1 AATATTAGAATATATTAGTATAGTTTTCAA
1432938 TGTGGTGTAG
Statistics
Matches: 198, Mismatches: 18, Indels: 21
0.84 0.08 0.09
Matches are distributed among these distances:
46 5 0.03
47 65 0.33
48 72 0.36
49 14 0.07
50 2 0.01
51 4 0.02
52 2 0.01
53 11 0.06
54 1 0.01
55 17 0.09
56 5 0.03
ACGTcount: A:0.36, C:0.03, G:0.16, T:0.46
Consensus pattern (48 bp):
AATATTAGAATATATTAGTATAGTTTTCAAATGTAGTATATGGTTTTA
Found at i:1432790 original size:95 final size:94
Alignment explanation
Indices: 1432663--1432940 Score: 376
Period size: 95 Copynumber: 2.9 Consensus size: 94
1432653 TATTAGTATT
* *
1432663 AATATAAGAATATATTAGTATAGTTTTCAAATGTAGTATATGGTTTTAAATATTCGAATATATTA
1 AATATTAGAATATATTAGTATAGTTTTCAAATGTAGTATATGGTTTTAAATATTAGAATATATTA
1432728 GTATAGTTTTCAATGTAGTATATGGTTTAA
66 GTATAGTTTTCAATGTAGTATATGGTTT-A
1432758 AATATTAGAATATATTAGTATAGTTTTCAAATGTAGTATATGGTTTTAAATATTAGAATATATTA
1 AATATTAGAATATATTAGTATAGTTTTCAAATGTAGTATATGGTTTTAAATATTAGAATATATTA
* *
1432823 GTATAGTTTTCAATGTAGTGTATGGTTTT
66 GTATAGTTTTCAATGTAGTATATGGTTTA
* * * * * *
1432852 AATTTTCAGATTATGTATTAGTATATGTAGTGCGTAATTTTTAGTATATGGTTTTAAATATTAGA
1 AATATT-AGA--ATATATTAGTATA-GT-TTTC--AA-ATGTAGTATATGGTTTTAAATATTAGA
*
1432917 ATATAGTAGTATAGTTTTCAATGT
58 ATATATTAGTATAGTTTTCAATGT
1432941 GGTGTAGTGT
Statistics
Matches: 164, Mismatches: 11, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
94 5 0.03
95 93 0.57
97 12 0.07
98 2 0.01
99 2 0.01
101 2 0.01
102 48 0.29
ACGTcount: A:0.35, C:0.03, G:0.16, T:0.46
Consensus pattern (94 bp):
AATATTAGAATATATTAGTATAGTTTTCAAATGTAGTATATGGTTTTAAATATTAGAATATATTA
GTATAGTTTTCAATGTAGTATATGGTTTA
Found at i:1436916 original size:23 final size:23
Alignment explanation
Indices: 1436886--1436946 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
1436876 CTGGTATAAA
1436886 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1436909 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1436932 TACACC-ATAGTGCCA
1 TGCACCGA-AGTGCCA
1436947 TATATGCTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 1 0.03
23 33 0.97
ACGTcount: A:0.30, C:0.28, G:0.25, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:1443736 original size:23 final size:23
Alignment explanation
Indices: 1443710--1443763 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
1443700 AAATGCACGG
1443710 AAGTGCCACGTAGAATTACACCA
1 AAGTGCCACGTAGAATTACACCA
* * *
1443733 AAGTGCCGCGTAGAATTGCACCG
1 AAGTGCCACGTAGAATTACACCA
*
1443756 TAGTGCCA
1 AAGTGCCA
1443764 TTTATACTTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.31, C:0.26, G:0.24, T:0.19
Consensus pattern (23 bp):
AAGTGCCACGTAGAATTACACCA
Found at i:1447305 original size:20 final size:20
Alignment explanation
Indices: 1447280--1447325 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
1447270 TCTAGAAGAT
1447280 TCTTGATTAATGAAGCACGA
1 TCTTGATTAATGAAGCACGA
1447300 TCTTGATTAATGAAGCACGA
1 TCTTGATTAATGAAGCACGA
1447320 TCTTGA
1 TCTTGA
1447326 ATTACTTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Consensus pattern (20 bp):
TCTTGATTAATGAAGCACGA
Found at i:1450524 original size:17 final size:17
Alignment explanation
Indices: 1450499--1450531 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1450489 TTAAAAATGT
*
1450499 AATCGTAATTTTAAATA
1 AATCATAATTTTAAATA
1450516 AATCATAATTTTAAAT
1 AATCATAATTTTAAAT
1450532 TAAGGGTAAA
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:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (17 bp):
AATCATAATTTTAAATA
Found at i:1452830 original size:2 final size:2
Alignment explanation
Indices: 1452823--1452867 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
1452813 AAAGTATAAC
1452823 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1452864 AT AT
1 AT AT
1452868 GAAATAAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1455128 original size:16 final size:16
Alignment explanation
Indices: 1455098--1455144 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
1455088 AAAATTATTC
*
1455098 ATTAACATTATTTTAAA
1 ATTAA-ATTAATTTAAA
1455115 ATTAAATTAATTTAAA
1 ATTAAATTAATTTAAA
*
1455131 TTTAAATTGAATTT
1 ATTAAATT-AATTT
1455145 TTCTCATATC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 17 0.63
17 10 0.37
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (16 bp):
ATTAAATTAATTTAAA
Found at i:1466672 original size:5 final size:5
Alignment explanation
Indices: 1466649--1466684 Score: 54
Period size: 5 Copynumber: 6.8 Consensus size: 5
1466639 TTTGGTTTCG
1466649 TTATAA TTATA TTATTA TTATA TTATA TTATA TTAT
1 TTAT-A TTATA TTA-TA TTATA TTATA TTATA TTAT
1466685 TATAATTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 20 0.69
6 9 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTATA
Done.