Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397269.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_12.1, 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: 5666189
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 144833 characters in sequence are not A, C, G, or T
File 6 of 14
Found at i:2129063 original size:23 final size:23
Alignment explanation
Indices: 2129021--2129064 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2129011 ATCAGTACTT
*
2129021 AATACTAGTAGGGTTATTAATCA
1 AATACTAGTAGGGTGATTAATCA
*
2129044 AATACTAGTAGGGTGCTTAAT
1 AATACTAGTAGGGTGATTAAT
2129065 GTATGCAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.34
Consensus pattern (23 bp):
AATACTAGTAGGGTGATTAATCA
Found at i:2131184 original size:35 final size:35
Alignment explanation
Indices: 2131138--2131212 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
2131128 TACTTGATGA
* * * *
2131138 AAATTGTTTAATTAAGTTGTTGGGCTTAATTAATT
1 AAATTGTTTAATTAAATTATTAGGCCTAATTAATT
*
2131173 AAATTGTTTAATTAAATTATTAGGCCTAATTGATT
1 AAATTGTTTAATTAAATTATTAGGCCTAATTAATT
2131208 AAATT
1 AAATT
2131213 AAACAATTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (35 bp):
AAATTGTTTAATTAAATTATTAGGCCTAATTAATT
Found at i:2139962 original size:2 final size:2
Alignment explanation
Indices: 2139955--2139979 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2139945 CAATGCTTGA
2139955 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
2139980 TTTTTTTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2144543 original size:53 final size:53
Alignment explanation
Indices: 2144480--2144596 Score: 225
Period size: 53 Copynumber: 2.2 Consensus size: 53
2144470 GCTAATCAGA
2144480 CTATCAATAAACATTATACACAGCCAAAACTAGCAAAAGAAGAAAAGCTCAAG
1 CTATCAATAAACATTATACACAGCCAAAACTAGCAAAAGAAGAAAAGCTCAAG
*
2144533 CTATCAATAAACATTATACACAGCCAAAACTAGCAAAAGAAGAAAGGCTCAAG
1 CTATCAATAAACATTATACACAGCCAAAACTAGCAAAAGAAGAAAAGCTCAAG
2144586 CTATCAATAAA
1 CTATCAATAAA
2144597 ACCGCAGGAC
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 63 1.00
ACGTcount: A:0.52, C:0.21, G:0.11, T:0.16
Consensus pattern (53 bp):
CTATCAATAAACATTATACACAGCCAAAACTAGCAAAAGAAGAAAAGCTCAAG
Found at i:2149294 original size:13 final size:14
Alignment explanation
Indices: 2149271--2149300 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2149261 TTATTTTAAA
2149271 ATTTAAAAAATTTT
1 ATTTAAAAAATTTT
*
2149285 ATTTAAAAATTTTT
1 ATTTAAAAAATTTT
2149299 AT
1 AT
2149301 ATTTTTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTTAAAAAATTTT
Found at i:2149306 original size:22 final size:22
Alignment explanation
Indices: 2149247--2149325 Score: 86
Period size: 22 Copynumber: 3.6 Consensus size: 22
2149237 AAGTTCAATC
*
2149247 AAATTTCTATATTTTTATTTTA
1 AAATTTTTATATTTTTATTTTA
** * * *
2149269 AAATTTAAAAAATTTTATTTAA
1 AAATTTTTATATTTTTATTTTA
*
2149291 AAATTTTTATATTTTTATTTTC
1 AAATTTTTATATTTTTATTTTA
*
2149313 AAATTCTTATATT
1 AAATTTTTATATT
2149326 ATTTGAAAGA
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (22 bp):
AAATTTTTATATTTTTATTTTA
Found at i:2149477 original size:23 final size:22
Alignment explanation
Indices: 2149435--2149483 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
2149425 AATTTGACCT
2149435 TTATTAATTTTTATAATTATAA
1 TTATTAATTTTTATAATTATAA
*
2149457 TTATATAA-TTTTATTATT-T-A
1 TTAT-TAATTTTTATAATTATAA
2149477 TTATTAA
1 TTATTAA
2149484 ATTAAAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 3 0.12
20 5 0.20
21 1 0.04
22 13 0.52
23 3 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TTATTAATTTTTATAATTATAA
Found at i:2149660 original size:21 final size:21
Alignment explanation
Indices: 2149622--2149672 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
2149612 TGTTTTTTCT
2149622 TTTTTAAA-TATATAAAAATAA
1 TTTTTAAATTATATAAAAA-AA
*
2149643 TTTTTAAATTA-ATCAAAAAA
1 TTTTTAAATTATATAAAAAAA
*
2149663 TATTTAAATT
1 TTTTTAAATT
2149673 TTTTTTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 11 0.41
21 14 0.52
22 2 0.07
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
TTTTTAAATTATATAAAAAAA
Found at i:2154666 original size:2 final size:2
Alignment explanation
Indices: 2154654--2154687 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2154644 TGGAATTATG
*
2154654 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2154688 AATGCTTTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2156209 original size:17 final size:17
Alignment explanation
Indices: 2156187--2156229 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
2156177 TTTAAGTCTC
* *
2156187 TTCTTTTAAAAATATTG
1 TTCTTTTAAAAAAATTA
2156204 TTC-TTTAAAAAAATTA
1 TTCTTTTAAAAAAATTA
*
2156220 TTTTTTTAAA
1 TTCTTTTAAA
2156230 GAGTTTTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (17 bp):
TTCTTTTAAAAAAATTA
Found at i:2156393 original size:18 final size:20
Alignment explanation
Indices: 2156365--2156401 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2156355 TTAAAATTAA
2156365 AATTAAAATATAA-AAATTT
1 AATTAAAATATAATAAATTT
2156384 AATT-AAATATAATAAATT
1 AATTAAAATATAATAAATT
2156402 ATATAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AATTAAAATATAATAAATTT
Found at i:2156410 original size:19 final size:18
Alignment explanation
Indices: 2156368--2156410 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
2156358 AAATTAAAAT
2156368 TAAAATATAAAAATTTAA
1 TAAAATATAAAAATTTAA
*
2156386 TTAAATATAATAAA-TTATA
1 TAAAATATAA-AAATTTA-A
2156405 TAAAAT
1 TAAAAT
2156411 TTTATTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAAATATAAAAATTTAA
Found at i:2168355 original size:5 final size:5
Alignment explanation
Indices: 2168345--2168374 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
2168335 TTAGTTACAT
2168345 AATAA AATAA AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA AATAA
2168375 TTTAATTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:2168376 original size:56 final size:56
Alignment explanation
Indices: 2168305--2168455 Score: 180
Period size: 56 Copynumber: 2.7 Consensus size: 56
2168295 ACAACCTAAG
* ** *
2168305 ATAAGATAAATTAATTTAATCTGGATACATTTAGTTACATAATAAAATAAAATAAA
1 ATAAGATAAAATAATTTAATCTAAATACACTTAGTTACATAATAAAATAAAATAAA
* * * * *
2168361 ATAAAATAAAATAATTTAATTTAAATACACTT-GATTACATGATAAATTAAGATAAA
1 ATAAGATAAAATAATTTAATCTAAATACACTTAG-TTACATAATAAAATAAAATAAA
* *
2168417 ATAAGATAAACTAACTTAATCTAAATACACTTA-TTACAT
1 ATAAGATAAAATAATTTAATCTAAATACACTTAGTTACAT
2168456 TCACGACTTT
Statistics
Matches: 80, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
55 7 0.09
56 73 0.91
ACGTcount: A:0.53, C:0.08, G:0.05, T:0.34
Consensus pattern (56 bp):
ATAAGATAAAATAATTTAATCTAAATACACTTAGTTACATAATAAAATAAAATAAA
Found at i:2189310 original size:24 final size:22
Alignment explanation
Indices: 2189277--2189324 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
2189267 CATTATTGCA
*
2189277 TTTAATTATAAACTTTTTAAATAT
1 TTTAACTAT-AACTTTTTAAA-AT
*
2189301 TTTAACTATAATTTTTTAAAAT
1 TTTAACTATAACTTTTTAAAAT
2189323 TT
1 TT
2189325 AAAAGATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 4 0.18
23 10 0.45
24 8 0.36
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTAACTATAACTTTTTAAAAT
Found at i:2189333 original size:22 final size:23
Alignment explanation
Indices: 2189290--2189336 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
2189280 AATTATAAAC
* **
2189290 TTTTTAAATATTTTAACTATAAT
1 TTTTTAAATATTTAAAAGATAAT
2189313 TTTTTAAA-ATTTAAAAGATAAT
1 TTTTTAAATATTTAAAAGATAAT
2189335 TT
1 TT
2189337 AAAACAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
TTTTTAAATATTTAAAAGATAAT
Found at i:2197108 original size:18 final size:18
Alignment explanation
Indices: 2197085--2197122 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2197075 TCTTTAAATT
**
2197085 AATTTTATCGATTCTTTA
1 AATTTTATAAATTCTTTA
2197103 AATTTTATAAATTCTTTA
1 AATTTTATAAATTCTTTA
2197121 AA
1 AA
2197123 CAACTTATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.53
Consensus pattern (18 bp):
AATTTTATAAATTCTTTA
Found at i:2198320 original size:15 final size:15
Alignment explanation
Indices: 2198296--2198330 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2198286 AAATTAACTT
*
2198296 TTAATGAAAATTAAA
1 TTAATCAAAATTAAA
2198311 TTAATCAAAATTAAA
1 TTAATCAAAATTAAA
*
2198326 ATAAT
1 TTAAT
2198331 GGTCCGAATC
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:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (15 bp):
TTAATCAAAATTAAA
Found at i:2206533 original size:17 final size:18
Alignment explanation
Indices: 2206511--2206544 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2206501 AAATTACACG
2206511 TCATATT-AAAAAAAGTA
1 TCATATTGAAAAAAAGTA
*
2206528 TCATATTGAATAAAAGT
1 TCATATTGAAAAAAAGT
2206545 TATAACACGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.06, G:0.09, T:0.32
Consensus pattern (18 bp):
TCATATTGAAAAAAAGTA
Found at i:2209613 original size:2 final size:2
Alignment explanation
Indices: 2209608--2209632 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2209598 TGTGTGTGTG
2209608 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2209633 GTTTTTTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2211427 original size:107 final size:107
Alignment explanation
Indices: 2211241--2211450 Score: 384
Period size: 107 Copynumber: 2.0 Consensus size: 107
2211231 TAACAAGGGA
*
2211241 AATTATTAAGGAGGATAATGAGGCATGGTCCTCTAAAATTTGGATCAAAAAAATCTCTTTTTCCC
1 AATTATTAAGGAGGATAATGAGGCATGGTCCTCTAAAATTTGGATCAAAAAAATCTCTTCTTCCC
2211306 CCTTTTTTAATATTAAATGAGGGATAAATAGCTTGTTTTGTT
66 CCTTTTTTAATATTAAATGAGGGATAAATAGCTTGTTTTGTT
*
2211348 AATTATTAAGGAGGATAATGAGGCATGGTCCTCTAAAATTTGGATCAAAAAAATCTCTTCTTCCT
1 AATTATTAAGGAGGATAATGAGGCATGGTCCTCTAAAATTTGGATCAAAAAAATCTCTTCTTCCC
**
2211413 TTTTTTTTAATATTAAATGAGGGATAAATAGCTTGTTT
66 CCTTTTTTAATATTAAATGAGGGATAAATAGCTTGTTT
2211451 CATACTTTAG
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
107 99 1.00
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (107 bp):
AATTATTAAGGAGGATAATGAGGCATGGTCCTCTAAAATTTGGATCAAAAAAATCTCTTCTTCCC
CCTTTTTTAATATTAAATGAGGGATAAATAGCTTGTTTTGTT
Found at i:2212044 original size:26 final size:22
Alignment explanation
Indices: 2211993--2212045 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 22
2211983 ATTTAGTAAC
2211993 TTTT-TTATTAAAATAATAATA
1 TTTTATTATTAAAATAATAATA
*
2212014 ATTTATTATTAAATATCAATATGATA
1 TTTTATTATTAAA-AT-AATA--ATA
2212040 TTTTAT
1 TTTTAT
2212046 ATAATAAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
21 3 0.12
22 8 0.32
23 2 0.08
24 4 0.16
26 8 0.32
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTTATTATTAAAATAATAATA
Found at i:2214637 original size:2 final size:2
Alignment explanation
Indices: 2214630--2214658 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2214620 GGATTGAGTT
2214630 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 T
2214659 GAATATTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2223605 original size:5 final size:5
Alignment explanation
Indices: 2223595--2223748 Score: 54
Period size: 5 Copynumber: 31.4 Consensus size: 5
2223585 ACCGAGAATA
* * * *
2223595 TATTT TATTTT TATTT T-TTAA TATAT T-TTT TATAT TA-TA TATTT TATTT
1 TATTT TA-TTT TATTT TATT-T TATTT TATTT TATTT TATTT TATTT TATTT
* * * * * * * *
2223644 TAATT TATTT TA-CT TATAT TATATA AATGTT AATTT T-TTA TATTT TACTT
1 TATTT TATTT TATTT TATTT TAT-TT TAT-TT TATTT TATTT TATTT TATTT
* * * * *
2223694 TATTT TA-AT T-TTT TATTCT TATAT TA-TA TATTT TATTT TAATA TATTT
1 TATTT TATTT TATTT TATT-T TATTT TATTT TATTT TATTT TATTT TATTT
2223742 TATTT TA
1 TATTT TA
2223749 ATTATAACAT
Statistics
Matches: 105, Mismatches: 32, Indels: 24
0.65 0.20 0.15
Matches are distributed among these distances:
4 19 0.18
5 70 0.67
6 16 0.15
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.68
Consensus pattern (5 bp):
TATTT
Found at i:2223621 original size:12 final size:14
Alignment explanation
Indices: 2223592--2223663 Score: 55
Period size: 14 Copynumber: 5.4 Consensus size: 14
2223582 TTTACCGAGA
*
2223592 ATATATTTTAT-TT
1 ATATTTTTTATATT
*
2223605 TTATTTTTTA-A-T
1 ATATTTTTTATATT
2223617 ATATTTTTTATATT
1 ATATTTTTTATATT
* *
2223631 ATATATTTTATTTT
1 ATATTTTTTATATT
2223645 A-ATTTATTT-TACTT
1 ATATTT-TTTATA-TT
2223659 ATATT
1 ATATT
2223664 ATATAAATGT
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
12 10 0.22
13 13 0.28
14 20 0.43
15 3 0.07
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.69
Consensus pattern (14 bp):
ATATTTTTTATATT
Found at i:2223652 original size:15 final size:15
Alignment explanation
Indices: 2223634--2223751 Score: 77
Period size: 15 Copynumber: 8.0 Consensus size: 15
2223624 TTATATTATA
2223634 TATTTTATTTTAATT
1 TATTTTATTTTAATT
*
2223649 TATTTTA-CTT-ATAT
1 TATTTTATTTTAAT-T
** *
2223663 TATATAAATGTTAATT
1 TAT-TTTATTTTAATT
*
2223679 T-TTTATATTTTACTT
1 TATTT-TATTTTAATT
*
2223694 TATTTTAATTT--TT
1 TATTTTATTTTAATT
* *
2223707 TATTCTTATATT-ATA
1 TATT-TTATTTTAATT
*
2223722 TATTTTATTTTAATA
1 TATTTTATTTTAATT
2223737 TATTTTATTTTAATT
1 TATTTTATTTTAATT
2223752 ATAACATTAT
Statistics
Matches: 80, Mismatches: 14, Indels: 18
0.71 0.12 0.16
Matches are distributed among these distances:
13 8 0.10
14 18 0.22
15 45 0.56
16 7 0.09
17 2 0.03
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.67
Consensus pattern (15 bp):
TATTTTATTTTAATT
Found at i:2223753 original size:33 final size:33
Alignment explanation
Indices: 2223692--2223754 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
2223682 TATATTTTAC
2223692 TTTATTTTAATTTTTTATTCTTATATTATATAT
1 TTTATTTTAATTTTTTATTCTTATATTATATAT
2223725 TTTATTTTAATATATTTTATT-TTA-ATTATA
1 TTTATTTTAAT-T-TTTTATTCTTATATTATA
2223755 ACATTATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 17 0.61
34 4 0.14
35 7 0.25
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (33 bp):
TTTATTTTAATTTTTTATTCTTATATTATATAT
Found at i:2225441 original size:29 final size:28
Alignment explanation
Indices: 2225397--2225542 Score: 130
Period size: 29 Copynumber: 5.1 Consensus size: 28
2225387 GTTAATAAAG
* *
2225397 AAAAGTTGTACGTGAACAAGTACAAGAA
1 AAAAGCTGTACGTGAACAGGTACAAGAA
*
2225425 AAGAAGCTGTACATGAACAGGTACAAGAGA
1 AA-AAGCTGTACGTGAACAGGTACAAGA-A
*
2225455 AAAAGCTGTACGTGAACAGGTATAAGAGA
1 AAAAGCTGTACGTGAACAGGTACAAGA-A
** * * ** *
2225484 GGAAGTTATATATGAACGGGTACAAGAGA
1 AAAAGCTGTACGTGAACAGGTACAAGA-A
* * *
2225513 AAAGGCTGTACGTGAACAAGTATAAGAA
1 AAAAGCTGTACGTGAACAGGTACAAGAA
2225541 AA
1 AA
2225543 CAAAAAAAAA
Statistics
Matches: 93, Mismatches: 23, Indels: 4
0.77 0.19 0.03
Matches are distributed among these distances:
28 5 0.05
29 85 0.91
30 3 0.03
ACGTcount: A:0.47, C:0.10, G:0.26, T:0.17
Consensus pattern (28 bp):
AAAAGCTGTACGTGAACAGGTACAAGAA
Found at i:2225499 original size:58 final size:58
Alignment explanation
Indices: 2225397--2225542 Score: 202
Period size: 58 Copynumber: 2.5 Consensus size: 58
2225387 GTTAATAAAG
* * *
2225397 AAAAGTTGTACGTGAACAAGTACAAGAAAAGAAGCTGTACATGAACAGGTACAAGAGA
1 AAAAGCTGTACGTGAACAAGTATAAGAAAAGAAGCTATACATGAACAGGTACAAGAGA
* * * * * *
2225455 AAAAGCTGTACGTGAACAGGTATAAGAGAGGAAGTTATATATGAACGGGTACAAGAGA
1 AAAAGCTGTACGTGAACAAGTATAAGAAAAGAAGCTATACATGAACAGGTACAAGAGA
*
2225513 AAAGGCTGTACGTGAACAAGTATAAGAAAA
1 AAAAGCTGTACGTGAACAAGTATAAGAAAA
2225543 CAAAAAAAAA
Statistics
Matches: 75, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 75 1.00
ACGTcount: A:0.47, C:0.10, G:0.26, T:0.17
Consensus pattern (58 bp):
AAAAGCTGTACGTGAACAAGTATAAGAAAAGAAGCTATACATGAACAGGTACAAGAGA
Found at i:2226728 original size:33 final size:33
Alignment explanation
Indices: 2226691--2226772 Score: 164
Period size: 33 Copynumber: 2.5 Consensus size: 33
2226681 TATTTACGCC
2226691 CTTTGAATTTCACCAAAATTCAATGATTTTTGA
1 CTTTGAATTTCACCAAAATTCAATGATTTTTGA
2226724 CTTTGAATTTCACCAAAATTCAATGATTTTTGA
1 CTTTGAATTTCACCAAAATTCAATGATTTTTGA
2226757 CTTTGAATTTCACCAA
1 CTTTGAATTTCACCAA
2226773 GAACTCTTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (33 bp):
CTTTGAATTTCACCAAAATTCAATGATTTTTGA
Found at i:2227556 original size:56 final size:56
Alignment explanation
Indices: 2227470--2227583 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
2227460 TAATAAACAT
2227470 TTCTAAAACCTAACTAAAAAGAGATTAACTATATTTAGTGCCACATATCCTCTCTA
1 TTCTAAAACCTAACTAAAAAGAGATTAACTATATTTAGTGCCACATATCCTCTCTA
2227526 TTCTAAAACCTAACTAAAAAGAGATTAACTATATTTAGTGCCACATATCCTCTCTA
1 TTCTAAAACCTAACTAAAAAGAGATTAACTATATTTAGTGCCACATATCCTCTCTA
2227582 TT
1 TT
2227584 ATCATATACA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.39, C:0.21, G:0.07, T:0.33
Consensus pattern (56 bp):
TTCTAAAACCTAACTAAAAAGAGATTAACTATATTTAGTGCCACATATCCTCTCTA
Found at i:2230573 original size:23 final size:22
Alignment explanation
Indices: 2230517--2230590 Score: 78
Period size: 23 Copynumber: 3.3 Consensus size: 22
2230507 TTTTAATATT
*
2230517 AAATATTATTTAATTATAATAA
1 AAATATTATTAAATTATAATAA
** *
2230539 AAAGT-TTAATTATCTTCTAATACA
1 AAA-TATT-ATTAAATTATAATA-A
2230563 AAATATTATTAAATTATAATAA
1 AAATATTATTAAATTATAATAA
2230585 AAATAT
1 AAATAT
2230591 GTTTTTATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
22 12 0.29
23 23 0.56
24 6 0.15
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (22 bp):
AAATATTATTAAATTATAATAA
Found at i:2230749 original size:23 final size:22
Alignment explanation
Indices: 2230721--2230774 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
2230711 CTCATTATAG
2230721 TATTTTTATTTTTTAATTAAAAAA
1 TATTTTTATTTTTT-A-TAAAAAA
* * *
2230745 T-TTTTAAATTTTTATAAAAAG
1 TATTTTTATTTTTTATAAAAAA
2230766 TATTTTTAT
1 TATTTTTAT
2230775 CATTTATCAT
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
21 7 0.29
22 6 0.25
23 10 0.42
24 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
TATTTTTATTTTTTATAAAAAA
Found at i:2230756 original size:22 final size:22
Alignment explanation
Indices: 2230722--2230773 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
2230712 TCATTATAGT
**
2230722 ATTTTTATTTTTTAATTAAAAA-
1 ATTTTTAAATTTTAA-TAAAAAG
*
2230744 ATTTTTAAATTTTTATAAAAAG
1 ATTTTTAAATTTTAATAAAAAG
2230766 TATTTTTA
1 -ATTTTTA
2230774 TCATTTATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 6 0.24
22 12 0.48
23 7 0.28
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
ATTTTTAAATTTTAATAAAAAG
Found at i:2231823 original size:20 final size:20
Alignment explanation
Indices: 2231798--2231839 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2231788 TTATATTAAT
2231798 AAATTT-TAAATTTATCAAAA
1 AAATTTATAAATTTAT-AAAA
*
2231818 AAATTTATAATTTTATAAAA
1 AAATTTATAAATTTATAAAA
2231838 AA
1 AA
2231840 TGATCCGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
AAATTTATAAATTTATAAAA
Found at i:2236690 original size:24 final size:26
Alignment explanation
Indices: 2236641--2236690 Score: 61
Period size: 24 Copynumber: 2.0 Consensus size: 26
2236631 TATATACTTT
*
2236641 ATTTATAATTATAAAATATACAAATA
1 ATTTATAATTATAAAATAAACAAATA
2236667 ATTTA-AA-TATAAAA-AAACATAATA
1 ATTTATAATTATAAAATAAACA-AATA
2236691 GTTATTCCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 4 0.18
24 11 0.50
25 2 0.09
26 5 0.23
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (26 bp):
ATTTATAATTATAAAATAAACAAATA
Found at i:2239201 original size:2 final size:2
Alignment explanation
Indices: 2239194--2239222 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2239184 TTTCTAATCA
2239194 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2239223 TGCTAGCTCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2245276 original size:41 final size:41
Alignment explanation
Indices: 2245221--2245303 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
2245211 ACAGCAGATA
**
2245221 CAGCAGAGAGGTCGTTGTTTAGTTTTTCAACCAAACACTAG
1 CAGCAGAGAGGTCGTTGAGTAGTTTTTCAACCAAACACTAG
*
2245262 CAGCAGAGAGGTCGTTGAGTAGTTTTTCAACCAAACCCTAG
1 CAGCAGAGAGGTCGTTGAGTAGTTTTTCAACCAAACACTAG
2245303 C
1 C
2245304 CTAGAATAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (41 bp):
CAGCAGAGAGGTCGTTGAGTAGTTTTTCAACCAAACACTAG
Found at i:2250162 original size:25 final size:25
Alignment explanation
Indices: 2250133--2250184 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
2250123 AGGAGTGACA
2250133 AGTAATTATAGAAGATCATGAAA-TG
1 AGTAATTATAGAAGATCAT-AAAGTG
* *
2250158 AGTAATTATTGAAGGTCATAAAGTG
1 AGTAATTATAGAAGATCATAAAGTG
2250183 AG
1 AG
2250185 CCAATAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 3 0.12
25 21 0.88
ACGTcount: A:0.44, C:0.04, G:0.23, T:0.29
Consensus pattern (25 bp):
AGTAATTATAGAAGATCATAAAGTG
Found at i:2251039 original size:42 final size:42
Alignment explanation
Indices: 2250926--2251119 Score: 210
Period size: 42 Copynumber: 4.8 Consensus size: 42
2250916 CAAAAATGGA
* *
2250926 AAAAAAGAAAAGAAAAATAATTCCAAAATCTAAGACTAAATG
1 AAAAAAGAAAAGAAAAATAATTCCAAAATTTGAGACTAAATG
* *
2250968 AAAAAAGAAAAGAAAAATAATTCCAAAATTTGGGCCTAAATG
1 AAAAAAGAAAAGAAAAATAATTCCAAAATTTGAGACTAAATG
*
2251010 CAAAAAGAAAAGAAAAATAATTCCAAAATTTGA-ACT-AA-G
1 AAAAAAGAAAAGAAAAATAATTCCAAAATTTGAGACTAAATG
* **
2251049 ------GAAAAGAAAAATAATTCTAAAATTTGAG-CTAAGGAAA
1 AAAAAAGAAAAGAAAAATAATTCCAAAATTTGAGACTAA--ATG
**
2251086 AAAAAAGAAAAGAAAAATAATTCTGAAATTTGAG
1 AAAAAAGAAAAGAAAAATAATTCCAAAATTTGAG
2251120 TTAAAGAAGA
Statistics
Matches: 131, Mismatches: 10, Indels: 21
0.81 0.06 0.13
Matches are distributed among these distances:
33 28 0.21
34 1 0.01
36 1 0.01
39 1 0.01
40 2 0.02
41 2 0.02
42 69 0.53
43 27 0.21
ACGTcount: A:0.60, C:0.08, G:0.13, T:0.19
Consensus pattern (42 bp):
AAAAAAGAAAAGAAAAATAATTCCAAAATTTGAGACTAAATG
Found at i:2251057 original size:33 final size:33
Alignment explanation
Indices: 2251016--2251091 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 33
2251006 AATGCAAAAA
2251016 GAAAAGAAAAATAATTCCAAAATTTGAACTAAG
1 GAAAAGAAAAATAATTCCAAAATTTGAACTAAG
* *
2251049 GAAAAGAAAAATAATTCTAAAATTTGAGCTAAG
1 GAAAAGAAAAATAATTCCAAAATTTGAACTAAG
2251082 GAAAA-AAAAA
1 GAAAAGAAAAA
2251092 GAAAAGAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 5 0.12
33 36 0.88
ACGTcount: A:0.61, C:0.07, G:0.13, T:0.20
Consensus pattern (33 bp):
GAAAAGAAAAATAATTCCAAAATTTGAACTAAG
Found at i:2251118 original size:76 final size:75
Alignment explanation
Indices: 2250974--2251118 Score: 202
Period size: 76 Copynumber: 1.9 Consensus size: 75
2250964 AATGAAAAAA
* ***
2250974 GAAAAGAAAAATAATTCCAAAATTTGGGCCTAAATGCAAAAAGAAAAGAAAAATAATTCCAAAAT
1 GAAAAGAAAAATAATTCCAAAATTTGAGCCTAAAAAAAAAAAGAAAAGAAAAATAATTCCAAAAT
2251039 TTGAACTAAG
66 TTGAACTAAG
* **
2251049 GAAAAGAAAAATAATTCTAAAATTTGAG-CTAAGGAAAAAAAAAGAAAAGAAAAATAATTCTGAA
1 GAAAAGAAAAATAATTCCAAAATTTGAGCCTAA--AAAAAAAAAGAAAAGAAAAATAATTCCAAA
2251113 ATTTGA
64 ATTTGA
2251119 GTTAAAGAAG
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
74 4 0.07
75 26 0.43
76 31 0.51
ACGTcount: A:0.58, C:0.08, G:0.14, T:0.21
Consensus pattern (75 bp):
GAAAAGAAAAATAATTCCAAAATTTGAGCCTAAAAAAAAAAAGAAAAGAAAAATAATTCCAAAAT
TTGAACTAAG
Found at i:2251199 original size:58 final size:58
Alignment explanation
Indices: 2251083--2251202 Score: 145
Period size: 58 Copynumber: 2.1 Consensus size: 58
2251073 TGAGCTAAGG
** * * **
2251083 AAAAAAAAAGAAAAGAAAAATAATTCTGAAATTTGAGTTAAAGAAGAAAGAGCTAAGA
1 AAAAAAAAAGAAAAGAAAAATAATTCCAAAATCTGAGCTAAAGAAGAAAGAGAAAAGA
*
2251141 AAAAAAAAAGAAAAGAAAAGTAATTCCAAAATCTGAGACTAAATGAA-AAA-AGAAAAGA
1 AAAAAAAAAGAAAAGAAAAATAATTCCAAAATCTGAG-CTAAA-GAAGAAAGAGAAAAGA
2251199 AAAA
1 AAAA
2251203 TAATTCCAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
58 43 0.81
59 7 0.13
60 3 0.06
ACGTcount: A:0.66, C:0.05, G:0.15, T:0.14
Consensus pattern (58 bp):
AAAAAAAAAGAAAAGAAAAATAATTCCAAAATCTGAGCTAAAGAAGAAAGAGAAAAGA
Found at i:2251207 original size:42 final size:42
Alignment explanation
Indices: 2251144--2251330 Score: 190
Period size: 42 Copynumber: 4.8 Consensus size: 42
2251134 GCTAAGAAAA
* *
2251144 AAAAAAGAAAAGAAAAGTAATTCCAAAATCTGAGACTAAATG
1 AAAAAAGAAAAGAAAAATAATTCCAAAATTTGAGACTAAATG
*
2251186 AAAAAAGAAAAGAAAAATAATTCCAAAATTTG-GTCCTAAATG
1 AAAAAAGAAAAGAAAAATAATTCCAAAATTTGAG-ACTAAATG
*
2251228 CAAAAAGAAAAGAAAAATAATTCCAAAATTTGA-ACT-AA-G
1 AAAAAAGAAAAGAAAAATAATTCCAAAATTTGAGACTAAATG
*
2251267 ---AAAG---A-AAAAATAATTCCAAAATTTGAG--TTAA-G
1 AAAAAAGAAAAGAAAAATAATTCCAAAATTTGAGACTAAATG
* *
2251299 -GAAAA-AAAAGAAAAATAATTCTAAAATTTGAG
1 AAAAAAGAAAAGAAAAATAATTCCAAAATTTGAG
2251331 TTTGAAAAAA
Statistics
Matches: 129, Mismatches: 6, Indels: 25
0.81 0.04 0.16
Matches are distributed among these distances:
31 1 0.01
32 24 0.19
33 1 0.01
34 3 0.02
36 5 0.04
37 21 0.16
39 1 0.01
40 2 0.02
41 3 0.02
42 68 0.53
ACGTcount: A:0.59, C:0.08, G:0.12, T:0.20
Consensus pattern (42 bp):
AAAAAAGAAAAGAAAAATAATTCCAAAATTTGAGACTAAATG
Found at i:2251268 original size:32 final size:32
Alignment explanation
Indices: 2251232--2251329 Score: 108
Period size: 32 Copynumber: 2.9 Consensus size: 32
2251222 TAAATGCAAA
2251232 AAGAAAAGAAAAATAATTCCAAAATTTGAACT
1 AAGAAAAGAAAAATAATTCCAAAATTTGAACT
**
2251264 AAG-AAAGAAAAAATAATTCCAAAATTTGAGTT
1 AAGAAAAG-AAAAATAATTCCAAAATTTGAACT
*
2251296 AAGGAAAAAAAAGAAAAATAATTCTAAAATTTGA
1 AA-G----AAAAGAAAAATAATTCCAAAATTTGA
2251330 GTTTGAAAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
31 4 0.07
32 27 0.48
33 1 0.02
37 20 0.36
38 4 0.07
ACGTcount: A:0.60, C:0.06, G:0.11, T:0.22
Consensus pattern (32 bp):
AAGAAAAGAAAAATAATTCCAAAATTTGAACT
Found at i:2251269 original size:74 final size:69
Alignment explanation
Indices: 2251194--2251329 Score: 186
Period size: 69 Copynumber: 1.9 Consensus size: 69
2251184 TGAAAAAAGA
2251194 AAAG-AAAAATAATTCCAAAATTTG-GTCCTAAATGCAAAAAGAAAAGAAAAATAATTCCAAAAT
1 AAAGAAAAAATAATTCCAAAATTTGAGT--T-AA-G-AAAAA-AAAAGAAAAATAATTCCAAAAT
2251257 TTGAACTAAG
60 TTGAACTAAG
* *
2251267 AAAGAAAAAATAATTCCAAAATTTGAGTTAAGGAAAAAAAAGAAAAATAATTCTAAAATTTGA
1 AAAGAAAAAATAATTCCAAAATTTGAGTTAAGAAAAAAAAAGAAAAATAATTCCAAAATTTGA
2251330 GTTTGAAAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 8
0.86 0.03 0.12
Matches are distributed among these distances:
69 25 0.42
70 4 0.07
71 1 0.02
72 2 0.03
73 5 0.08
74 20 0.34
75 2 0.03
ACGTcount: A:0.58, C:0.08, G:0.11, T:0.23
Consensus pattern (69 bp):
AAAGAAAAAATAATTCCAAAATTTGAGTTAAGAAAAAAAAAGAAAAATAATTCCAAAATTTGAAC
TAAG
Found at i:2251318 original size:37 final size:38
Alignment explanation
Indices: 2251267--2251350 Score: 102
Period size: 37 Copynumber: 2.2 Consensus size: 38
2251257 TTGAACTAAG
*
2251267 AAAGAAAAAATAATTCCAAAATTTGAGTTAAGGAAAA-A
1 AAAG-AAAAATAATTCCAAAATTTGAGTTAAGAAAAAGA
* *
2251305 AAAGAAAAATAATTCTAAAATTTGAGTT-TGAAAAA-A
1 AAAGAAAAATAATTCCAAAATTTGAGTTAAGAAAAAGA
2251341 AAAGGAAAAA
1 AAA-GAAAAA
2251351 AAAGAAAAGA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
36 9 0.21
37 29 0.69
38 4 0.10
ACGTcount: A:0.62, C:0.04, G:0.13, T:0.21
Consensus pattern (38 bp):
AAAGAAAAATAATTCCAAAATTTGAGTTAAGAAAAAGA
Found at i:2251339 original size:32 final size:32
Alignment explanation
Indices: 2251235--2251343 Score: 98
Period size: 32 Copynumber: 3.3 Consensus size: 32
2251225 ATGCAAAAAG
**
2251235 AAAAGAAAAATAATTCCAAAATTTGA-ACT-A
1 AAAAGAAAAATAATTCCAAAATTTGAGTTTGA
*
2251265 AGAAAGAAAAAATAATTCCAAAATTTGAGTTAAGGAAAA
1 A-AAAG-AAAAATAATTCCAAAATTTGAGTT--TG---A
*
2251304 AAAAGAAAAATAATTCTAAAATTTGAGTTTGA
1 AAAAGAAAAATAATTCCAAAATTTGAGTTTGA
2251336 AAAA-AAAA
1 AAAAGAAAA
2251344 GGAAAAAAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 17
0.75 0.06 0.20
Matches are distributed among these distances:
30 1 0.02
31 8 0.12
32 26 0.40
35 1 0.02
37 23 0.35
38 4 0.06
39 2 0.03
ACGTcount: A:0.61, C:0.06, G:0.11, T:0.23
Consensus pattern (32 bp):
AAAAGAAAAATAATTCCAAAATTTGAGTTTGA
Found at i:2251350 original size:74 final size:75
Alignment explanation
Indices: 2251183--2251350 Score: 170
Period size: 74 Copynumber: 2.3 Consensus size: 75
2251173 CTGAGACTAA
*
2251183 ATGAAAAAAGAAAAGAAAAATAATTCCAAAATTTGGTCCTAAATGCAAAAAGAAAAGAAAAATAA
1 ATGAAAAAA-AAAGGAAAAATAATTCCAAAATTTGGT-CTAAATGCAAAAAGAAAAGAAAAATAA
2251248 TTCCAAAATTTG
64 TTCCAAAATTTG
** * * *
2251260 A--ACTAAGAAAGAAAAAATAATTCCAAAATTTGAGT-T-AA-G-GAAAA-AAAAGAAAAATAAT
1 ATGAAAAAAAAAGGAAAAATAATTCCAAAATTTG-GTCTAAATGCAAAAAGAAAAGAAAAATAAT
*
2251318 TCTAAAATTTG
65 TCCAAAATTTG
2251329 AGTTTGAAAAAAAAAGGAAAAA
1 A---TGAAAAAAAAAGGAAAAA
2251351 AAAGAAAAGA
Statistics
Matches: 74, Mismatches: 11, Indels: 15
0.74 0.11 0.15
Matches are distributed among these distances:
69 25 0.34
70 4 0.05
71 1 0.01
72 2 0.03
73 1 0.01
74 35 0.47
75 5 0.07
77 1 0.01
ACGTcount: A:0.60, C:0.07, G:0.12, T:0.21
Consensus pattern (75 bp):
ATGAAAAAAAAAGGAAAAATAATTCCAAAATTTGGTCTAAATGCAAAAAGAAAAGAAAAATAATT
CCAAAATTTG
Found at i:2255258 original size:21 final size:21
Alignment explanation
Indices: 2255234--2255273 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2255224 TAAAACTCCC
2255234 AAAGAAGACACAGAGAAAAAG
1 AAAGAAGACACAGAGAAAAAG
* *
2255255 AAAGAAGAGACGGAGAAAA
1 AAAGAAGACACAGAGAAAA
2255274 GTGAAAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.65, C:0.07, G:0.28, T:0.00
Consensus pattern (21 bp):
AAAGAAGACACAGAGAAAAAG
Found at i:2259976 original size:34 final size:34
Alignment explanation
Indices: 2259933--2259999 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
2259923 TTAATTGTAG
*
2259933 TGTATATTGATTAATTCACGGGTTGTTGGTGTTT
1 TGTATATTGATTAATTCACGGGTTATTGGTGTTT
*
2259967 TGTATATTGATTGATTCACGGGTTATTGGTGTT
1 TGTATATTGATTAATTCACGGGTTATTGGTGTT
2260000 CTTATTTTCG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.18, C:0.06, G:0.27, T:0.49
Consensus pattern (34 bp):
TGTATATTGATTAATTCACGGGTTATTGGTGTTT
Found at i:2265774 original size:2 final size:2
Alignment explanation
Indices: 2265769--2265798 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2265759 GTGTACCAGA
2265769 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
2265799 TATCTAGCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2268630 original size:34 final size:34
Alignment explanation
Indices: 2268558--2268630 Score: 103
Period size: 34 Copynumber: 2.1 Consensus size: 34
2268548 AAGGAAACTT
* *
2268558 TGTAACATTTAGTGTTAAAGCTTTGAACGTGACG
1 TGTAACATATAGTGTTAAAGCTTTGAACGTGACA
*
2268592 TGTAACATATAGTGTTAAAGCTTT-AACCTTGACA
1 TGTAACATATAGTGTTAAAGCTTTGAA-CGTGACA
2268626 TGTAA
1 TGTAA
2268631 TATCTGCTAC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
33 2 0.06
34 33 0.94
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (34 bp):
TGTAACATATAGTGTTAAAGCTTTGAACGTGACA
Found at i:2269359 original size:27 final size:27
Alignment explanation
Indices: 2269303--2269368 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
2269293 TAAACGCTAA
* * * * *
2269303 CATATAACAATTTTTTTTTCAACATGG
1 CATATAAAAATATTTTTTTAAAAATAG
2269330 CATATAAAAATATTTTTTTAAAAATAG
1 CATATAAAAATATTTTTTTAAAAATAG
* *
2269357 CATGTAATAATA
1 CATATAAAAATA
2269369 ACATTTTTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (27 bp):
CATATAAAAATATTTTTTTAAAAATAG
Found at i:2269484 original size:21 final size:22
Alignment explanation
Indices: 2269460--2269504 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
2269450 TTTTCATAGT
*
2269460 AGAAATAAAGTTTAAAAT-AAA
1 AGAAATAAACTTTAAAATCAAA
**
2269481 AGAAATTTACTTTAAAATCAAA
1 AGAAATAAACTTTAAAATCAAA
2269503 AG
1 AG
2269505 GTAAATATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.60, C:0.04, G:0.09, T:0.27
Consensus pattern (22 bp):
AGAAATAAACTTTAAAATCAAA
Found at i:2273659 original size:24 final size:24
Alignment explanation
Indices: 2273632--2273683 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
2273622 TGCTAACAAC
*
2273632 GGTGGTGATGCTTGCGCTGAAACT
1 GGTGGTGATACTTGCGCTGAAACT
* * *
2273656 GGTGGTGGTACTTGTGCTGACACT
1 GGTGGTGATACTTGCGCTGAAACT
2273680 GGTG
1 GGTG
2273684 CTGGTGCAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.13, C:0.15, G:0.40, T:0.31
Consensus pattern (24 bp):
GGTGGTGATACTTGCGCTGAAACT
Found at i:2273688 original size:24 final size:24
Alignment explanation
Indices: 2273642--2273688 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2273632 GGTGGTGATG
*
2273642 CTTGCGCTGAAACTGGTGGTGGTA
1 CTTGCGCTGAAACTGGTGCTGGTA
* *
2273666 CTTGTGCTGACACTGGTGCTGGT
1 CTTGCGCTGAAACTGGTGCTGGT
2273689 GCAGGCGCTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.13, C:0.19, G:0.36, T:0.32
Consensus pattern (24 bp):
CTTGCGCTGAAACTGGTGCTGGTA
Found at i:2278305 original size:15 final size:15
Alignment explanation
Indices: 2278281--2278415 Score: 70
Period size: 15 Copynumber: 9.1 Consensus size: 15
2278271 TAATATTATA
2278281 ATTAAAATAAAAAAT
1 ATTAAAATAAAAAAT
*
2278296 ATTAACATAAAATATAT
1 ATTAAAATAAAA-A-AT
2278313 AATATAAAA-ATAAAAA-
1 -AT-TAAAATA-AAAAAT
2278329 ATTAAAATAAAAAA-
1 ATTAAAATAAAAAAT
* * **
2278343 A-TATAACAAATTAT
1 ATTAAAATAAAAAAT
*
2278357 ATTTAAAA-AATAAAT
1 A-TTAAAATAAAAAAT
*
2278372 A-TAAAATAAATAAT
1 ATTAAAATAAAAAAT
* *
2278386 ATTATAATAATAAAT
1 ATTAAAATAAAAAAT
*
2278401 A--AAAATAAAATAT
1 ATTAAAATAAAAAAT
2278414 AT
1 AT
2278416 GATATTAAAA
Statistics
Matches: 90, Mismatches: 18, Indels: 25
0.68 0.14 0.19
Matches are distributed among these distances:
13 23 0.26
14 18 0.20
15 30 0.33
16 5 0.06
17 3 0.03
18 4 0.04
19 7 0.08
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (15 bp):
ATTAAAATAAAAAAT
Found at i:2278316 original size:20 final size:19
Alignment explanation
Indices: 2278269--2278413 Score: 59
Period size: 20 Copynumber: 7.4 Consensus size: 19
2278259 AAAAATATTT
2278269 TATAATATTATAATTAAAATA
1 TATAATATTA-AA-TAAAATA
* *
2278290 AAAAATATTAACATAAAATA
1 TATAATATTAA-ATAAAATA
* *
2278310 TATAATATAAAAATAAAAAA
1 TATAATAT-TAAATAAAATA
*
2278330 T-TAA-AATAAA-AAAATA
1 TATAATATTAAATAAAATA
* * *
2278346 TA-ACAAATTATATTTAAAAAA
1 TATA-ATATTA-A-ATAAAATA
*
2278367 TA-AATATAAAATAAATAATA
1 TATAATATTAAAT-AA-AATA
*
2278387 TTATAATAATAAATAAAA-A
1 -TATAATATTAAATAAAATA
*
2278406 TAAAATAT
1 TATAATAT
2278414 ATGATATTAA
Statistics
Matches: 92, Mismatches: 20, Indels: 27
0.66 0.14 0.19
Matches are distributed among these distances:
16 7 0.08
17 4 0.04
18 11 0.12
19 8 0.09
20 31 0.34
21 23 0.25
22 8 0.09
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (19 bp):
TATAATATTAAATAAAATA
Found at i:2278332 original size:48 final size:43
Alignment explanation
Indices: 2278280--2278389 Score: 116
Period size: 48 Copynumber: 2.5 Consensus size: 43
2278270 ATAATATTAT
2278280 AATTAAAATAAAAAATATTAACATAAAATATATAATATAAAAATAAAA
1 AATTAAAATAAAAAATATTAAC--AAAATATAT-ATA-AAAAAT-AAA
* *
2278328 AATTAAAATAAAAAA-ATATAACAAATTATATTTAAAAAATAAA
1 AATTAAAATAAAAAATAT-TAACAAAATATATATAAAAAATAAA
* *
2278371 TA-TAAAATAAATAATATTA
1 AATTAAAATAAAAAATATTA
2278390 TAATAATAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
42 13 0.23
43 6 0.11
44 6 0.11
45 2 0.04
46 8 0.14
47 2 0.04
48 19 0.34
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (43 bp):
AATTAAAATAAAAAATATTAACAAAATATATATAAAAAATAAA
Found at i:2278333 original size:33 final size:33
Alignment explanation
Indices: 2278272--2278428 Score: 113
Period size: 33 Copynumber: 4.6 Consensus size: 33
2278262 AATATTTTAT
*
2278272 AATATTATAAT-T-AAAATAAAAAATATTAACATAA
1 AATA-TATAATATAAAAATAAAAAATA--AAAATAA
*
2278306 AATATATAATATAAAAATAAAAAATTAAAATAAA
1 AATATATAATATAAAAATAAAAAATAAAAAT-AA
* * * *
2278340 AAAATATAACA-AATTATATTTAAAAAATAAATATAA
1 AATATATAATATAA--A-A-ATAAAAAATAAAAATAA
* * * *
2278376 AATAAATAATATTATAATAATAAATAAAAATAA
1 AATATATAATATAAAAATAAAAAATAAAAATAA
*
2278409 AATATATGATATTAAAAATA
1 AATATATAATA-TAAAAATA
2278429 TATTTAAGAG
Statistics
Matches: 95, Mismatches: 19, Indels: 18
0.72 0.14 0.14
Matches are distributed among these distances:
33 35 0.37
34 23 0.24
35 13 0.14
36 11 0.12
37 13 0.14
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.31
Consensus pattern (33 bp):
AATATATAATATAAAAATAAAAAATAAAAATAA
Found at i:2278362 original size:29 final size:29
Alignment explanation
Indices: 2278313--2278408 Score: 72
Period size: 29 Copynumber: 3.2 Consensus size: 29
2278303 TAAAATATAT
* *
2278313 AATATAA-AAATAAAAAATTAAAATAAAAA
1 AATATAACAAAT-AATATTTAAAATAAAAA
*
2278342 AATATAACAAATTATATTTAAAA-AATAAA
1 AATATAACAAATAATATTTAAAATAA-AAA
* * *
2278371 TATAAAATAAATAATATTATAATAATAAATAA
1 AATATAACAAATAATATT-TAA-AATAAA-AA
2278403 AA-ATAA
1 AATATAA
2278409 AATATATGAT
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
28 2 0.04
29 32 0.62
30 7 0.13
31 6 0.12
32 5 0.10
ACGTcount: A:0.71, C:0.01, G:0.00, T:0.28
Consensus pattern (29 bp):
AATATAACAAATAATATTTAAAATAAAAA
Found at i:2278658 original size:15 final size:15
Alignment explanation
Indices: 2278638--2278679 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
2278628 TTACAATAAT
*
2278638 ATTACTTGTAATCAC
1 ATTACTTATAATCAC
*
2278653 ATTACTTATAATCGC
1 ATTACTTATAATCAC
2278668 ATTACATTATAA
1 ATTAC-TTATAA
2278680 AATACCAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 18 0.75
16 6 0.25
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.40
Consensus pattern (15 bp):
ATTACTTATAATCAC
Found at i:2279768 original size:19 final size:20
Alignment explanation
Indices: 2279741--2279787 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
2279731 TAACTATTAA
*
2279741 AATACTTATTACT-AATAGT
1 AATATTTATTACTAAATAGT
*
2279760 AATATTTATTATTAAAATAGT
1 AATATTTATTACT-AAATAGT
2279781 AATATTT
1 AATATTT
2279788 TGATGGTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 11 0.46
21 13 0.54
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (20 bp):
AATATTTATTACTAAATAGT
Found at i:2282469 original size:2 final size:2
Alignment explanation
Indices: 2282464--2282500 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2282454 GCTTGATCTA
2282464 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2282501 AGAAGTAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2286696 original size:108 final size:113
Alignment explanation
Indices: 2286566--2286793 Score: 306
Period size: 119 Copynumber: 2.0 Consensus size: 113
2286556 TATTTTTTAG
*
2286566 TTTCTATATATTTATATGCAACAAG-TT-TTT-TA-TT-TTGTTAGTATTCTATATT-TTAATAA
1 TTTCTATATATTTATATGCAACAAGTTTATTTATATTTATTATTAGTATTCTATATTGTT-ATAA
* * *
2286625 ATTCACTCTTAGTAAAATTTTTAAAATTCATCATCTATGTGTAAGATAA
65 ATTCACTCTCAATAAAATTTTTAAAATTCATCATCTATGTATAAGATAA
2286674 TTTCTATATATTTATATGCAACAAGTTTTTTATTTATATTTTTTATTATTAGTATTCTATATTGT
1 TTTCTATATATTTATATGCAACAAG---TTTATTTATA---TTTATTATTAGTATTCTATATTGT
*
2286739 TATAAATTCACTGTCAATAAAATTTTTAAAATTCATCATCTATGTATAAGATAA
60 TATAAATTCACTCTCAATAAAATTTTTAAAATTCATCATCTATGTATAAGATAA
2286793 T
1 T
2286794 AGCTCGTAAA
Statistics
Matches: 103, Mismatches: 5, Indels: 13
0.85 0.04 0.11
Matches are distributed among these distances:
108 25 0.24
112 2 0.02
113 3 0.03
114 2 0.02
118 2 0.02
119 67 0.65
120 2 0.02
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.50
Consensus pattern (113 bp):
TTTCTATATATTTATATGCAACAAGTTTATTTATATTTATTATTAGTATTCTATATTGTTATAAA
TTCACTCTCAATAAAATTTTTAAAATTCATCATCTATGTATAAGATAA
Found at i:2289650 original size:3 final size:3
Alignment explanation
Indices: 2289638--2289671 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
2289628 ATATTTAGTT
2289638 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2289672 GAGTTAAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2300960 original size:15 final size:15
Alignment explanation
Indices: 2300923--2300974 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
2300913 ATTGAAAAAC
2300923 ATAAATAAATATAAAT
1 ATAAATAAA-ATAAAT
2300939 A-ATAATAATAAT-AAT
1 ATA-AATAA-AATAAAT
*
2300954 ATAAATAAATTAAAT
1 ATAAATAAAATAAAT
2300969 ATAAAT
1 ATAAAT
2300975 TTTAACTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
14 2 0.06
15 19 0.61
16 9 0.29
17 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
ATAAATAAAATAAAT
Found at i:2301058 original size:19 final size:19
Alignment explanation
Indices: 2301034--2301077 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
2301024 ATGGATGACG
2301034 AAATTTAAAAAATTAAAAA
1 AAATTTAAAAAATTAAAAA
* * *
2301053 AAATTTAAAAATTTGAATA
1 AAATTTAAAAAATTAAAAA
2301072 AAATTT
1 AAATTT
2301078 GTAAAATCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (19 bp):
AAATTTAAAAAATTAAAAA
Found at i:2302738 original size:27 final size:27
Alignment explanation
Indices: 2302700--2302756 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
2302690 CATCACTTTT
2302700 AAGCATGGAAGCGT-CT-AGAGGTGTTCC
1 AAGCATGGAAGC-TCCTAAG-GGTGTTCC
2302727 AAGCATGGAAGCTCCTAAGGGTGTTCC
1 AAGCATGGAAGCTCCTAAGGGTGTTCC
2302754 AAG
1 AAG
2302757 TGCGGAAGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
26 1 0.04
27 25 0.89
28 2 0.07
ACGTcount: A:0.28, C:0.19, G:0.32, T:0.21
Consensus pattern (27 bp):
AAGCATGGAAGCTCCTAAGGGTGTTCC
Found at i:2305475 original size:52 final size:52
Alignment explanation
Indices: 2305392--2305490 Score: 126
Period size: 52 Copynumber: 1.9 Consensus size: 52
2305382 TATTAGTCAT
* * ** *
2305392 AAGCTTTATGACTCATTTCTTGGCCTTAGTTTGCTTTTCACAAATTGGCCGC
1 AAGCTTTATCACTCATTTATTGGCCACAGTTTGCTATTCACAAATTGGCCGC
* * *
2305444 AAGCTTTATCTCTCATTTATTGGTCACAGTTTTCTATTCACAAATTG
1 AAGCTTTATCACTCATTTATTGGCCACAGTTTGCTATTCACAAATTG
2305491 ATCGCTGACT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 39 1.00
ACGTcount: A:0.22, C:0.21, G:0.14, T:0.42
Consensus pattern (52 bp):
AAGCTTTATCACTCATTTATTGGCCACAGTTTGCTATTCACAAATTGGCCGC
Found at i:2306547 original size:26 final size:27
Alignment explanation
Indices: 2306475--2306548 Score: 68
Period size: 26 Copynumber: 2.8 Consensus size: 27
2306465 AAAGAGCCCC
*
2306475 AGGGTGTTCCAAGC--GGAGAGCGCTCA
1 AGGGTGTTCCAAGCATGGA-AGCACTCA
*
2306501 AGGGTGTTTCAA--ATGTAGAAGCACTCA
1 AGGGTGTTCCAAGCATG--GAAGCACTCA
2306528 A-GGTGTTCCAAGCATGGAAGC
1 AGGGTGTTCCAAGCATGGAAGC
2306549 GTACATGGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
26 26 0.67
27 8 0.21
28 5 0.13
ACGTcount: A:0.28, C:0.19, G:0.32, T:0.20
Consensus pattern (27 bp):
AGGGTGTTCCAAGCATGGAAGCACTCA
Found at i:2314145 original size:43 final size:43
Alignment explanation
Indices: 2314098--2314184 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
2314088 TCTCACTTCA
2314098 CTATGCCTTGCTCTTTCTCCCTTTAATTCTTTCTTCCATAAAC
1 CTATGCCTTGCTCTTTCTCCCTTTAATTCTTTCTTCCATAAAC
2314141 CTATGCCTTGCTCTTTCTCCCTTTAATTCTTTCTTCCATAAAC
1 CTATGCCTTGCTCTTTCTCCCTTTAATTCTTTCTTCCATAAAC
2314184 C
1 C
2314185 CACACTTCTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.16, C:0.33, G:0.05, T:0.46
Consensus pattern (43 bp):
CTATGCCTTGCTCTTTCTCCCTTTAATTCTTTCTTCCATAAAC
Found at i:2321034 original size:30 final size:30
Alignment explanation
Indices: 2321000--2321112 Score: 106
Period size: 30 Copynumber: 3.8 Consensus size: 30
2320990 TTTAGTTTAA
2321000 AATAAAAATATGAAA-ATTTATTTGACTCAT
1 AATAAAAATAT-AAAGATTTATTTGACTCAT
* * *
2321030 AATAAAAGTATAAGGATTTATTT-AGCTCAA
1 AATAAAAATATAAAGATTTATTTGA-CTCAT
* * * *
2321060 AACAAAAATATAAAGACTTAATTGAAT-AT
1 AATAAAAATATAAAGATTTATTTGACTCAT
*
2321089 AATATAAAAAATAAAGATTTATTT
1 AATA-AAAATATAAAGATTTATTT
2321113 AAAATTTTTA
Statistics
Matches: 65, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
29 7 0.11
30 57 0.88
31 1 0.02
ACGTcount: A:0.53, C:0.05, G:0.08, T:0.34
Consensus pattern (30 bp):
AATAAAAATATAAAGATTTATTTGACTCAT
Found at i:2321050 original size:60 final size:60
Alignment explanation
Indices: 2320979--2321113 Score: 148
Period size: 60 Copynumber: 2.2 Consensus size: 60
2320969 ATAATTAGTT
* * * * * * * **
2320979 ATAAAAATTTATTTAGTTTAAAATAAAAATATGAAA-ATTTATTTGACTCATAATA-AAAGT
1 ATAAAGATTTATTTAGCTCAAAACAAAAATAT-AAAGACTTAATTGAAT-ATAATATAAAAA
*
2321039 ATAAGGATTTATTTAGCTCAAAACAAAAATATAAAGACTTAATTGAATATAATATAAAAA
1 ATAAAGATTTATTTAGCTCAAAACAAAAATATAAAGACTTAATTGAATATAATATAAAAA
2321099 ATAAAGATTTATTTA
1 ATAAAGATTTATTTA
2321114 AAATTTTTAA
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
59 9 0.15
60 53 0.85
ACGTcount: A:0.53, C:0.04, G:0.07, T:0.36
Consensus pattern (60 bp):
ATAAAGATTTATTTAGCTCAAAACAAAAATATAAAGACTTAATTGAATATAATATAAAAA
Found at i:2327762 original size:18 final size:18
Alignment explanation
Indices: 2327739--2327774 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2327729 GTATACTTAT
2327739 GACTGATCAAAACATGAA
1 GACTGATCAAAACATGAA
2327757 GACTGATCAAAACATGAA
1 GACTGATCAAAACATGAA
2327775 TGTGCTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.17
Consensus pattern (18 bp):
GACTGATCAAAACATGAA
Found at i:2337938 original size:2 final size:2
Alignment explanation
Indices: 2337933--2337962 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2337923 GCTTGTGCGT
2337933 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2337963 AAGATACCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2340939 original size:111 final size:111
Alignment explanation
Indices: 2340800--2341137 Score: 502
Period size: 111 Copynumber: 3.1 Consensus size: 111
2340790 CCAACCCTAT
** * * *
2340800 TTCCTTTCCACAATTCAATTCCTGTGCAATGTGCTCATTCTCCATTGCTAGCTCTGCCAGGTTGG
1 TTCCTTTCCACAATTTGATTCCTTTGCAATGAGCTCATTCTCTATTGCTAGCTCTGCCAGGTTGG
* *
2340865 AATTAGTCTTGGCTTCTGTTTCTCCATCTTCACAACCAGCATCAAG
66 AATTAGTCTTGGCTTCTGTTTCTCCCTCTTCACAACCAGCAGCAAG
* *
2340911 TTCCTTTCCACAATTTGATTCCTTTGCAATGAGCTCATTCTCTATAGCTAGCTCTGCCTGGTTGG
1 TTCCTTTCCACAATTTGATTCCTTTGCAATGAGCTCATTCTCTATTGCTAGCTCTGCCAGGTTGG
2340976 AATTAGT-TGTGGCTTCTGTTTCTCCCTCTTCACAACCAGCAGCAAG
66 AATTAGTCT-TGGCTTCTGTTTCTCCCTCTTCACAACCAGCAGCAAG
** *
2341022 TTCCTTTCTGCAATTTGATT-CTTGTGTAATGAGCTCATTCTCTATTGCTAGCTCTGCCAGGTTG
1 TTCCTTTCCACAATTTGATTCCTT-TGCAATGAGCTCATTCTCTATTGCTAGCTCTGCCAGGTTG
* * *
2341086 GAATTTGTCCTGGCTTCTGTTTCTCCCTCTTCATAACCAGCAGCAAG
65 GAATTAGTCTTGGCTTCTGTTTCTCCCTCTTCACAACCAGCAGCAAG
2341133 -TCCTT
1 TTCCTT
2341138 CAGAGAAGCT
Statistics
Matches: 207, Mismatches: 17, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
110 9 0.04
111 198 0.96
ACGTcount: A:0.18, C:0.27, G:0.17, T:0.38
Consensus pattern (111 bp):
TTCCTTTCCACAATTTGATTCCTTTGCAATGAGCTCATTCTCTATTGCTAGCTCTGCCAGGTTGG
AATTAGTCTTGGCTTCTGTTTCTCCCTCTTCACAACCAGCAGCAAG
Found at i:2352687 original size:47 final size:46
Alignment explanation
Indices: 2352634--2352734 Score: 143
Period size: 47 Copynumber: 2.2 Consensus size: 46
2352624 AGAGAAAATT
*
2352634 GAAGGAAAGAATCTTAATC-TAATTTTC-CCAGAGGAAAAGAGAAAGA
1 GAAGGAAAGAATCTTAATCTTAA--TTCGCCAAAGGAAAAGAGAAAGA
*
2352680 GAGAGGAAAGAATCTTAATCTTAATTCGCCAAAGGAAATGAGAAAGA
1 GA-AGGAAAGAATCTTAATCTTAATTCGCCAAAGGAAAAGAGAAAGA
2352727 GAAGGAAA
1 GAAGGAAA
2352735 ACTACGCAAG
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
46 11 0.22
47 36 0.72
48 3 0.06
ACGTcount: A:0.49, C:0.10, G:0.24, T:0.18
Consensus pattern (46 bp):
GAAGGAAAGAATCTTAATCTTAATTCGCCAAAGGAAAAGAGAAAGA
Found at i:2364201 original size:19 final size:19
Alignment explanation
Indices: 2364165--2364203 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2364155 AGTATGAAAT
**
2364165 TAAAATAATATTTTAATAA
1 TAAAATAATATTAAAATAA
2364184 TAAAATAATATTAAAATAA
1 TAAAATAATATTAAAATAA
2364203 T
1 T
2364204 GGTAGAGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAATAATATTAAAATAA
Found at i:2364382 original size:19 final size:19
Alignment explanation
Indices: 2364346--2364383 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2364336 AGTATAATAA
*
2364346 AAATATTTTATATATATTT
1 AAATATTTTATAGATATTT
2364365 AAATATTATTAT-GATATTT
1 AAATATT-TTATAGATATTT
2364384 TGATAGAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
AAATATTTTATAGATATTT
Found at i:2366221 original size:2 final size:2
Alignment explanation
Indices: 2366214--2366238 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2366204 TGAAATTGTG
2366214 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2366239 TTGAAAGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2372334 original size:19 final size:19
Alignment explanation
Indices: 2372301--2372337 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2372291 CCAATATTTA
**
2372301 AAAAAATGACTAAAAAAAG
1 AAAAAATGAAAAAAAAAAG
2372320 AAAAAATGAAAAAAAAAA
1 AAAAAATGAAAAAAAAAA
2372338 CAATGAGATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.81, C:0.03, G:0.08, T:0.08
Consensus pattern (19 bp):
AAAAAATGAAAAAAAAAAG
Found at i:2387915 original size:17 final size:17
Alignment explanation
Indices: 2387870--2387918 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
2387860 GAGATTTCCT
*
2387870 TTATTTTTTTCCCTTTA
1 TTATTTTTTTCTCTTTA
*
2387887 TTATTTTTTTCTCTTTG
1 TTATTTTTTTCTCTTTA
*
2387904 TTCTTTTTTTCTCTT
1 TTATTTTTTTCTCTT
2387919 GTTTTTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.06, C:0.16, G:0.02, T:0.76
Consensus pattern (17 bp):
TTATTTTTTTCTCTTTA
Found at i:2389951 original size:38 final size:38
Alignment explanation
Indices: 2389877--2389952 Score: 93
Period size: 38 Copynumber: 2.0 Consensus size: 38
2389867 AAAGATAAAA
* *
2389877 TTATTTTTTATTATAATATATAATTATTTATTTTAATT
1 TTATTTTTTATTATAATATATAATAATTTATATTAATT
*
2389915 TTATTTTATTTTTA-AATAT-TAATAATTTATAATTAATT
1 TTATTTT-TTATTATAATATATAATAATTTAT-ATTAATT
2389953 CAAAATATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 10 0.30
38 18 0.55
39 5 0.15
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (38 bp):
TTATTTTTTATTATAATATATAATAATTTATATTAATT
Found at i:2390068 original size:20 final size:19
Alignment explanation
Indices: 2389976--2390069 Score: 64
Period size: 20 Copynumber: 4.6 Consensus size: 19
2389966 AGTAATGTTT
2389976 AAATATTAATATTTTATTTA
1 AAAT-TTAATATTTTATTTA
* **
2389996 TAATTTAATCATTAACATTTTA
1 AAATTTAAT-ATT-TTA-TTTA
*
2390018 AAATCCTAATATTTTATTTA
1 AAAT-TTAATATTTTATTTA
*
2390038 TAATTTAAATATTATTA-TTA
1 AAATTT-AATATT-TTATTTA
2390058 AAATATTAATAT
1 AAAT-TTAATAT
2390070 AATTTTAATT
Statistics
Matches: 57, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
19 6 0.11
20 30 0.53
21 7 0.12
22 10 0.18
23 4 0.07
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATTTAATATTTTATTTA
Found at i:2390493 original size:23 final size:25
Alignment explanation
Indices: 2390449--2390498 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
2390439 TTATGATTCC
2390449 AATATTAATATTTTAATAAATTTAA
1 AATATTAATATTTTAATAAATTTAA
* *
2390474 AATATTAAT-TTTTTATAATTTTAA
1 AATATTAATATTTTAATAAATTTAA
2390498 A
1 A
2390499 CTTTTTTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
AATATTAATATTTTAATAAATTTAA
Found at i:2401380 original size:11 final size:11
Alignment explanation
Indices: 2401364--2401388 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2401354 CAGTTAAATA
2401364 TAATTATTTTT
1 TAATTATTTTT
2401375 TAATTATTTTT
1 TAATTATTTTT
2401386 TAA
1 TAA
2401389 ACATTGTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TAATTATTTTT
Found at i:2408737 original size:19 final size:20
Alignment explanation
Indices: 2408695--2408737 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
2408685 ATATTTTGAT
* *
2408695 AAAAAATAATATAAATAGTT
1 AAAAAATAATAAAAATAGTG
*
2408715 AAAAATTAATAAAAAT-GTG
1 AAAAAATAATAAAAATAGTG
2408734 AAAA
1 AAAA
2408738 GTGAAAGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (20 bp):
AAAAAATAATAAAAATAGTG
Found at i:2413015 original size:21 final size:21
Alignment explanation
Indices: 2412964--2413017 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
2412954 CTTTGTAAGT
* *
2412964 TTAATTTTAAAATATTTTTTA
1 TTAATTTTTAAATATTTTTAA
* *
2412985 TTATAATTTTAATTATTTTTAA
1 TTA-ATTTTTAAATATTTTTAA
2413007 TTAATTTTTAA
1 TTAATTTTTAA
2413018 CATAATTTGA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTAATTTTTAAATATTTTTAA
Found at i:2413886 original size:60 final size:59
Alignment explanation
Indices: 2413792--2413905 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 59
2413782 ACGAAGAATG
* * * *
2413792 CTTAAAATGTTCAAAAGTTTTTTTCATGTATCAAAAATCACTTCAAAATACTTAAAATA
1 CTTAAAACGTTCAAAAATATTTTTCATATATCAAAAATCACTTCAAAATACTTAAAATA
* *
2413851 CTTAAAACGTTCAAAAAATATTTTTCATATATCAAAAATTACTTTAAAATACTTA
1 CTTAAAACGTTC-AAAAATATTTTTCATATATCAAAAATCACTTCAAAATACTTA
2413906 GAGATTTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
59 11 0.23
60 37 0.77
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.38
Consensus pattern (59 bp):
CTTAAAACGTTCAAAAATATTTTTCATATATCAAAAATCACTTCAAAATACTTAAAATA
Found at i:2424528 original size:84 final size:84
Alignment explanation
Indices: 2424387--2424557 Score: 342
Period size: 84 Copynumber: 2.0 Consensus size: 84
2424377 GAACTAGGTT
2424387 TATGACTTACCTAAATTGTATTTCTATTAAGACCACAACTTTTAATCCTGTGGGAAGCCCACAAG
1 TATGACTTACCTAAATTGTATTTCTATTAAGACCACAACTTTTAATCCTGTGGGAAGCCCACAAG
2424452 ATTATCTGTCTTCGAAGAA
66 ATTATCTGTCTTCGAAGAA
2424471 TATGACTTACCTAAATTGTATTTCTATTAAGACCACAACTTTTAATCCTGTGGGAAGCCCACAAG
1 TATGACTTACCTAAATTGTATTTCTATTAAGACCACAACTTTTAATCCTGTGGGAAGCCCACAAG
2424536 ATTATCTGTCTTCGAAGAA
66 ATTATCTGTCTTCGAAGAA
2424555 TAT
1 TAT
2424558 TTGCGTTTGA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 87 1.00
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (84 bp):
TATGACTTACCTAAATTGTATTTCTATTAAGACCACAACTTTTAATCCTGTGGGAAGCCCACAAG
ATTATCTGTCTTCGAAGAA
Found at i:2442604 original size:15 final size:15
Alignment explanation
Indices: 2442586--2442616 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2442576 AGTAACATGA
2442586 GGTGTAGATGTTGAT
1 GGTGTAGATGTTGAT
*
2442601 GGTGTTGATGTTGAT
1 GGTGTAGATGTTGAT
2442616 G
1 G
2442617 TTGGTGTTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.42, T:0.42
Consensus pattern (15 bp):
GGTGTAGATGTTGAT
Found at i:2442844 original size:71 final size:71
Alignment explanation
Indices: 2442755--2442999 Score: 283
Period size: 71 Copynumber: 3.4 Consensus size: 71
2442745 TAATAATTCT
* * * *
2442755 AAACATTAATTCCCAAACATAATTCGTAATATTTAATTCTAGCATATTGCCAATTATTTTAATTG
1 AAACAATAATT-CTAAACATAATTCCTAATATTTAATTCTAGCATATTGCCAATCATTTTAATTG
2442820 AAAATCC
65 AAAATCC
* * *
2442827 AAACAATATTTATAAACATTAATTCCTAAAGATAATGTTAATTCTAGCATATTACCAATCATTTT
1 AAACAATAATTCTAAACA-TAATTCCT--A-AT-AT-TTAATTCTAGCATATTGCCAATCATTTT
2442892 AATTGAAAATCC
60 AATTGAAAATCC
* ** * * *
2442904 AAACAATAATTCTCAACATAATTTTTAATGTTTAATTCTAGTATATTGACAATCATTTTAATTGA
1 AAACAATAATTCTAAACATAATTCCTAATATTTAATTCTAGCATATTGCCAATCATTTTAATTGA
*
2442969 AAATCT
66 AAATCC
* *
2442975 AAATAATAATTCTCAACATAATTCC
1 AAACAATAATTCTAAACATAATTCC
2443000 CAAACATAAT
Statistics
Matches: 147, Mismatches: 20, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
71 63 0.43
72 17 0.12
73 2 0.01
74 2 0.01
75 2 0.01
76 8 0.05
77 53 0.36
ACGTcount: A:0.42, C:0.15, G:0.05, T:0.38
Consensus pattern (71 bp):
AAACAATAATTCTAAACATAATTCCTAATATTTAATTCTAGCATATTGCCAATCATTTTAATTGA
AAATCC
Found at i:2442877 original size:77 final size:76
Alignment explanation
Indices: 2442781--2443135 Score: 337
Period size: 84 Copynumber: 4.5 Consensus size: 76
2442771 ACATAATTCG
* * * * *
2442781 TAATATTTAATTCTAGCATATTGCCAATTATTTTAATTGAAAATCCAAACAATATTTATAAACAT
1 TAATGTTTAATTCTAGCATATTGCCAATCATTTTAATTGAAAATCCAAACAATAATTCTCAACA-
2442846 TAATTCCTAAAGA
65 TAATTCCTAAA-A
*
2442859 TAATG-TTAATTCTAGCATATTACCAATCATTTTAATTGAAAATCCAAACAATAATTCTCAACAT
1 TAATGTTTAATTCTAGCATATTGCCAATCATTTTAATTGAAAATCCAAACAATAATTCTCAACAT
*
2442923 AATT--T---T
66 AATTCCTAAAA
* * * *
2442929 TAATGTTTAATTCTAGTATATTGACAATCATTTTAATTGAAAATCTAAATAATAATTCTCAACAT
1 TAATGTTTAATTCTAGCATATTGCCAATCATTTTAATTGAAAATCCAAACAATAATTCTCAACAT
*
2442994 AATTCCCAAACATAA
66 AATT-CC-TA-A-AA
* *
2443009 TTCTTAATGTTTAATTCTAGCATATTGTCAATCATTTTAATTGAAAATCCAAATAATAATTCTCA
1 ----TAATGTTTAATTCTAGCATATTGCCAATCATTTTAATTGAAAATCCAAACAATAATTCTCA
*
2443074 ACAGAATTTCC-AAACA
62 ACATAA-TTCCTAAA-A
* * *
2443090 TAATTCTTAATATTAATTCTAGCATATTACTAATCATTTTAATTGA
1 TAA----T-GT-TTAATTCTAGCATATTGCCAATCATTTTAATTGA
2443136 TCGGTTTCTT
Statistics
Matches: 233, Mismatches: 22, Indels: 39
0.79 0.07 0.13
Matches are distributed among these distances:
70 5 0.02
71 58 0.25
74 1 0.00
76 5 0.02
77 56 0.24
78 4 0.02
80 1 0.00
81 3 0.01
82 2 0.01
83 31 0.13
84 65 0.28
85 2 0.01
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.39
Consensus pattern (76 bp):
TAATGTTTAATTCTAGCATATTGCCAATCATTTTAATTGAAAATCCAAACAATAATTCTCAACAT
AATTCCTAAAA
Found at i:2442997 original size:12 final size:13
Alignment explanation
Indices: 2442980--2443012 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
2442970 AATCTAAATA
2442980 ATAATTCTC-AAC
1 ATAATTCTCAAAC
*
2442992 ATAATTCCCAAAC
1 ATAATTCTCAAAC
2443005 ATAATTCT
1 ATAATTCT
2443013 TAATGTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.42, C:0.24, G:0.00, T:0.33
Consensus pattern (13 bp):
ATAATTCTCAAAC
Found at i:2443087 original size:84 final size:84
Alignment explanation
Indices: 2442918--2443135 Score: 350
Period size: 84 Copynumber: 2.6 Consensus size: 84
2442908 AATAATTCTC
* * *
2442918 AACATAATTTTTAATGTTTAATTCTAGTATATTGACAATCATTTTAATTGAAAATCTAAATAATA
1 AACATAATTCTTAATGTTTAATTCTAGCATATTGACAATCATTTTAATTGAAAATCCAAATAATA
*
2442983 ATTCTCAACATAATTCCCA
66 ATTCTCAACAGAATTCCCA
*
2443002 AACATAATTCTTAATGTTTAATTCTAGCATATTGTCAATCATTTTAATTGAAAATCCAAATAATA
1 AACATAATTCTTAATGTTTAATTCTAGCATATTGACAATCATTTTAATTGAAAATCCAAATAATA
*
2443067 ATTCTCAACAGAATTTCCA
66 ATTCTCAACAGAATTCCCA
*
2443086 AACATAATTCTTAAT-ATTAATTCTAGCATATT-ACTAATCATTTTAATTGA
1 AACATAATTCTTAATGTTTAATTCTAGCATATTGAC-AATCATTTTAATTGA
2443136 TCGGTTTCTT
Statistics
Matches: 125, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
82 1 0.01
83 31 0.25
84 93 0.74
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.40
Consensus pattern (84 bp):
AACATAATTCTTAATGTTTAATTCTAGCATATTGACAATCATTTTAATTGAAAATCCAAATAATA
ATTCTCAACAGAATTCCCA
Found at i:2449057 original size:23 final size:23
Alignment explanation
Indices: 2449031--2449079 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
2449021 TATGGAATAT
2449031 TGGGTTTCTGTCATATGGTATCA
1 TGGGTTTCTGTCATATGGTATCA
2449054 TGGGTTTCTGTCATATGGTATCA
1 TGGGTTTCTGTCATATGGTATCA
2449077 TGG
1 TGG
2449080 ATACTCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.16, C:0.12, G:0.29, T:0.43
Consensus pattern (23 bp):
TGGGTTTCTGTCATATGGTATCA
Found at i:2449162 original size:22 final size:22
Alignment explanation
Indices: 2449136--2449180 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2449126 CAGACACTGC
* *
2449136 TATATACATATACATACATACA
1 TATATACATATACACACACACA
*
2449158 TATATATATATACACACACACA
1 TATATACATATACACACACACA
2449180 T
1 T
2449181 GTATCTTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (22 bp):
TATATACATATACACACACACA
Found at i:2453655 original size:4 final size:4
Alignment explanation
Indices: 2453646--2453676 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
2453636 TCTTACCTTT
2453646 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
2453677 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:2464093 original size:19 final size:22
Alignment explanation
Indices: 2464052--2464103 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
2464042 GTTTAAAGGT
2464052 ATAATATTTAAAAAATTTCTAA
1 ATAATATTTAAAAAATTTCTAA
*
2464074 ATAAT-TTTTAAAAA-TT-TAA
1 ATAATATTTAAAAAATTTCTAA
2464093 ATAAATATTTA
1 AT-AATATTTA
2464104 TTTATTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 5 0.19
20 5 0.19
21 11 0.42
22 5 0.19
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
ATAATATTTAAAAAATTTCTAA
Found at i:2464103 original size:20 final size:21
Alignment explanation
Indices: 2464052--2464103 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
2464042 GTTTAAAGGT
2464052 ATAATATTTAAAAAATTTCTAA
1 ATAATATTT-AAAAATTTCTAA
*
2464074 ATAATTTTTAAAAA-TT-TAA
1 ATAATATTTAAAAATTTCTAA
2464093 ATAAATATTTA
1 AT-AATATTTA
2464104 TTTATTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 5 0.19
20 9 0.33
21 5 0.19
22 8 0.30
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
ATAATATTTAAAAATTTCTAA
Found at i:2464353 original size:15 final size:16
Alignment explanation
Indices: 2464330--2464363 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2464320 AATTTTTAAT
*
2464330 TAAATAAATAATATAA
1 TAAATAAATAATAAAA
2464346 TAAA-AAATAATAAAA
1 TAAATAAATAATAAAA
2464361 TAA
1 TAA
2464364 CTCTATCATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
TAAATAAATAATAAAA
Found at i:2464615 original size:35 final size:36
Alignment explanation
Indices: 2464573--2464655 Score: 114
Period size: 35 Copynumber: 2.3 Consensus size: 36
2464563 CTAAGCCCAC
* *
2464573 TATAATATATTATATCTTAACAACCCAATTTAATAA
1 TATAATATATTATATCTCAACAACCCAACTTAATAA
**
2464609 -ATAATATATTATATCTCAACAATTCAACTTAATAA
1 TATAATATATTATATCTCAACAACCCAACTTAATAA
*
2464644 TCTAATATATTA
1 TATAATATATTA
2464656 ATTAACAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
35 31 0.76
36 10 0.24
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (36 bp):
TATAATATATTATATCTCAACAACCCAACTTAATAA
Found at i:2467049 original size:79 final size:79
Alignment explanation
Indices: 2466911--2467067 Score: 210
Period size: 79 Copynumber: 2.0 Consensus size: 79
2466901 TTCTCAATCA
* * **
2466911 AGGATTTTCAATCCAATTTTACTAAAACCAGTAGAATTAACAATTTTCACCAAGTTTTTATAACT
1 AGGATTTTCAATCCAATTTTACTAAAACCAGTAGAATTAACAATTTTCACCAAGGTTTTACAAAA
2466976 TGAGCTTCTAACTT
66 TGAGCTTCTAACTT
* * * *
2466990 AGGATTTTCAATCTAATTTCT-CTAAAATCAGT-GAAATTAACAGTTTTCATCAAGGTTTTACAA
1 AGGATTTTCAATCCAATTT-TACTAAAACCAGTAG-AATTAACAATTTTCACCAAGGTTTTACAA
2467053 AATGAGCTTCTAACT
64 AATGAGCTTCTAACT
2467068 CAAGCTCTAA
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
78 1 0.01
79 66 0.97
80 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.38
Consensus pattern (79 bp):
AGGATTTTCAATCCAATTTTACTAAAACCAGTAGAATTAACAATTTTCACCAAGGTTTTACAAAA
TGAGCTTCTAACTT
Found at i:2470578 original size:14 final size:15
Alignment explanation
Indices: 2470561--2470589 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2470551 TAACAAAATA
2470561 TCTTCTTCT-TTTTT
1 TCTTCTTCTATTTTT
2470575 TCTTCTTCTATTTTT
1 TCTTCTTCTATTTTT
2470590 ACACTTCACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (15 bp):
TCTTCTTCTATTTTT
Found at i:2479958 original size:26 final size:25
Alignment explanation
Indices: 2479929--2479997 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 25
2479919 TGAATATATA
2479929 TAAAATTTA-AAATAT-TATTAAATTGT
1 TAAAATTTATAAATATATATT--ATT-T
*
2479955 TAAAATTTATAATTATATATTATTT
1 TAAAATTTATAAATATATATTATTT
2479980 TAAAATTTGATAAA-ATAT
1 TAAAATTT-ATAAATATAT
2479998 TAGAAAATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
25 13 0.34
26 16 0.42
27 5 0.13
28 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (25 bp):
TAAAATTTATAAATATATATTATTT
Found at i:2483305 original size:25 final size:25
Alignment explanation
Indices: 2483271--2483322 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
2483261 TAAACAGCGC
*
2483271 TGTACTTTGTACTTATATATGCATA
1 TGTACTTTGTACTTATAAATGCATA
2483296 TGTACTTTGTACTTATAAATGCATA
1 TGTACTTTGTACTTATAAATGCATA
2483321 TG
1 TG
2483323 CGATTTGATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.46
Consensus pattern (25 bp):
TGTACTTTGTACTTATAAATGCATA
Found at i:2483896 original size:2 final size:2
Alignment explanation
Indices: 2483889--2483928 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
2483879 GATAAACTCT
2483889 GA GA GA GA GA GA G- GA GA -A GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2483929 TGCATTTGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2487951 original size:67 final size:67
Alignment explanation
Indices: 2487834--2487959 Score: 225
Period size: 67 Copynumber: 1.9 Consensus size: 67
2487824 CAAAGTATGA
*
2487834 TTCCACTTAAATATGCTTTAGGCTAAAAGAGGATTTAATAACACAGGAATGAAAGGAGATAGTCT
1 TTCCACTTAAATATGCTTTAGGCTAAAAGAGGATTTAATAACACAAGAATGAAAGGAGATAGTCT
2487899 GG
66 GG
* *
2487901 TTCCACTTAAATATGCTTTAGGCTAAAAGAGGATTTACTAGCACAAGAATGAAAGGAGA
1 TTCCACTTAAATATGCTTTAGGCTAAAAGAGGATTTAATAACACAAGAATGAAAGGAGA
2487960 AACAAGTACA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 56 1.00
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (67 bp):
TTCCACTTAAATATGCTTTAGGCTAAAAGAGGATTTAATAACACAAGAATGAAAGGAGATAGTCT
GG
Found at i:2491211 original size:25 final size:25
Alignment explanation
Indices: 2491165--2491216 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 25
2491155 TTTTTGGTAT
* *
2491165 TAAAAAGTATCAAATATAAATATTA
1 TAAAAAGTATAAAATATAAATAATA
* * *
2491190 TAAAAAGTTTAAAATGTTAATAATA
1 TAAAAAGTATAAAATATAAATAATA
2491215 TA
1 TA
2491217 TAGTATACTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.35
Consensus pattern (25 bp):
TAAAAAGTATAAAATATAAATAATA
Found at i:2500202 original size:21 final size:21
Alignment explanation
Indices: 2500176--2500232 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
2500166 TTTTGGGTTG
*
2500176 TATCTATTGATAGCTGAAGAA
1 TATCTATTGATAGATGAAGAA
*
2500197 TATCTATTGATTGATGAAGAA
1 TATCTATTGATAGATGAAGAA
* *
2500218 CATCTATCGATAGAT
1 TATCTATTGATAGAT
2500233 AAACTCTAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.35
Consensus pattern (21 bp):
TATCTATTGATAGATGAAGAA
Found at i:2505679 original size:11 final size:11
Alignment explanation
Indices: 2505660--2505700 Score: 50
Period size: 10 Copynumber: 3.9 Consensus size: 11
2505650 TTTTTAAATA
*
2505660 ATAATAATAAT
1 ATAAAAATAAT
2505671 ATAAAAATAAT
1 ATAAAAATAAT
2505682 A-AAAAATAA-
1 ATAAAAATAAT
*
2505691 AAAAAAATAA
1 ATAAAAATAA
2505701 AAAAAAGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 1 0.04
10 16 0.57
11 11 0.39
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (11 bp):
ATAAAAATAAT
Found at i:2505694 original size:17 final size:18
Alignment explanation
Indices: 2505655--2505704 Score: 66
Period size: 17 Copynumber: 2.7 Consensus size: 18
2505645 CACTTTTTTT
2505655 AAATAATAATAATAATATAA
1 AAATAATAA-AA-AATATAA
2505675 AAATAATAAAAAATA-AA
1 AAATAATAAAAAATATAA
*
2505692 AAAAAATAAAAAA
1 AAATAATAAAAAA
2505705 AAGTGAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 14 0.48
18 4 0.14
19 2 0.07
20 9 0.31
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (18 bp):
AAATAATAAAAAATATAA
Found at i:2505714 original size:11 final size:10
Alignment explanation
Indices: 2505673--2505706 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
2505663 ATAATAATAT
*
2505673 AAAAATAATA
1 AAAAATAAAA
2505683 AAAAATAAAA
1 AAAAATAAAA
2505693 AAAAATAAAA
1 AAAAATAAAA
2505703 AAAA
1 AAAA
2505707 GTGAAAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:2505714 original size:20 final size:20
Alignment explanation
Indices: 2505655--2505706 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
2505645 CACTTTTTTT
* *
2505655 AAATAAT-AATAATAATATAA
1 AAATAATAAAAAATAA-AAAA
2505675 AAATAATAAAAAATAAAAAA
1 AAATAATAAAAAATAAAAAA
2505695 AAATAA-AAAAAA
1 AAATAATAAAAAA
2505707 GTGAAAAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 6 0.21
20 16 0.55
21 7 0.24
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (20 bp):
AAATAATAAAAAATAAAAAA
Found at i:2506346 original size:15 final size:15
Alignment explanation
Indices: 2506326--2506375 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
2506316 GACGTCGACC
2506326 AAAAGGAGAGGAAAA
1 AAAAGGAGAGGAAAA
2506341 AAAAGGA-AGAGAAAA
1 AAAAGGAGAG-GAAAA
* *
2506356 GAAA-GAGAGAAAGAA
1 AAAAGGAGAGGAA-AA
2506371 AAAAG
1 AAAAG
2506376 AAAAAGGGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
14 6 0.21
15 22 0.79
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (15 bp):
AAAAGGAGAGGAAAA
Found at i:2506355 original size:11 final size:11
Alignment explanation
Indices: 2506341--2506402 Score: 51
Period size: 11 Copynumber: 5.8 Consensus size: 11
2506331 GAGAGGAAAA
*
2506341 AAAAGGAAGAG
1 AAAAGAAAGAG
2506352 AAAAGAAAGAG
1 AAAAGAAAGAG
2506363 AGAAAGAAA-A-
1 A-AAAGAAAGAG
*
2506373 AAGAA-AAAGGG
1 AA-AAGAAAGAG
2506384 AAAA-AAAGAG
1 AAAAGAAAGAG
*
2506394 AGAAGAAAG
1 AAAAGAAAG
2506403 GCCAGTTAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
9 4 0.10
10 13 0.31
11 18 0.43
12 7 0.17
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (11 bp):
AAAAGAAAGAG
Found at i:2506386 original size:19 final size:19
Alignment explanation
Indices: 2506347--2506390 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
2506337 AAAAAAAAGG
* *
2506347 AAGAGAAAAGAAAGAGAGA
1 AAGAAAAAAGAAAAAGAGA
*
2506366 AAGAAAAAAGAAAAAGGGA
1 AAGAAAAAAGAAAAAGAGA
2506385 AA-AAAA
1 AAGAAAA
2506391 GAGAGAAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (19 bp):
AAGAAAAAAGAAAAAGAGA
Found at i:2507162 original size:4 final size:4
Alignment explanation
Indices: 2507153--2507212 Score: 51
Period size: 4 Copynumber: 16.0 Consensus size: 4
2507143 TGTATATAAC
*
2507153 AATA AATA AATA AATA AATA AA-A TAATA AAT- CATA AA-A TAATA AA-A
1 AATA AATA AATA AATA AATA AATA -AATA AATA AATA AATA -AATA AATA
2507199 AAT- AAT- AATA AATA
1 AATA AATA AATA AATA
2507213 CAAACAAGGT
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
3 13 0.28
4 32 0.68
5 2 0.04
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (4 bp):
AATA
Done.